Integrating paleoecology and genetics of bird populations in two sky island archipelagos

<p>Abstract</p> <p>Background</p> <p>Genetic tests of paleoecological hypotheses have been rare, partly because recent genetic divergence is difficult to detect and time. According to fossil plant data, continuous woodland in the southwestern USA and northern Mexico became fragmented during the last 10,000 years, as warming caused cool-adapted species to retreat to high elevations. Most genetic studies of resulting 'sky islands' have either failed to detect recent divergence or have found discordant evidence for ancient divergence. We test this paleoecological hypothesis for the region with intraspecific mitochondrial DNA and microsatellite data from sky-island populations of a sedentary bird, the Mexican jay (<it>Aphelocoma ultramarina</it>). We predicted that populations on different sky islands would share common, ancestral alleles that existed during the last glaciation, but that populations on each sky island, owing to their isolation, would contain unique variants of postglacial origin. We also predicted that divergence times estimated from corrected genetic distance and a coalescence model would post-date the last glacial maximum.</p> <p>Results</p> <p>Our results provide multiple independent lines of support for postglacial divergence, with the predicted pattern of shared and unique mitochondrial DNA haplotypes appearing in two independent sky-island archipelagos, and most estimates of divergence time based on corrected genetic distance post-dating the last glacial maximum. Likewise, an isolation model based on multilocus gene coalescence indicated postglacial divergence of five pairs of sky islands. In contrast to their similar recent histories, the two archipelagos had dissimilar historical patterns in that sky islands in Arizona showed evidence for older divergence, suggesting different responses to the last glaciation.</p> <p>Conclusion</p> <p>This study is one of the first to provide explicit support from genetic data for a postglacial divergence scenario predicted by one of the best paleoecological records in the world. Our results demonstrate that sky islands act as generators of genetic diversity at both recent and historical timescales and underscore the importance of thorough sampling and the use of loci with fast mutation rates to studies that test hypotheses concerning recent genetic divergence.</p

Vδ2+ T cell response to malaria correlates with protection from infection but is attenuated with repeated exposure.

Vδ2+ γδ T cells are semi-innate T cells that expand markedly following P. falciparum (Pf) infection in naïve adults, but are lost and become dysfunctional among children repeatedly exposed to malaria. The role of these cells in mediating clinical immunity (i.e. protection against symptoms) to malaria remains unclear. We measured Vδ2+ T cell absolute counts at acute and convalescent malaria timepoints (n = 43), and Vδ2+ counts, cellular phenotype, and cytokine production following in vitro stimulation at asymptomatic visits (n = 377), among children aged 6 months to 10 years living in Uganda. Increasing age was associated with diminished in vivo expansion following malaria, and lower Vδ2 absolute counts overall, among children living in a high transmission setting. Microscopic parasitemia and expression of the immunoregulatory markers Tim-3 and CD57 were associated with diminished Vδ2+ T cell pro-inflammatory cytokine production. Higher Vδ2 pro-inflammatory cytokine production was associated with protection from subsequent Pf infection, but also with an increased odds of symptoms once infected. Vδ2+ T cells may play a role in preventing malaria infection in children living in endemic settings; progressive loss and dysfunction of these cells may represent a disease tolerance mechanism that contributes to the development of clinical immunity to malaria

Developing Performance Indicators to Evaluate the Management Effectiveness of the Massachusetts Ocean Management Plan

In June 2009, the Massachusetts Executive Office of Energy and Environmental Affairs (EEA) released its draft Massachusetts Ocean Management Plan (draft plan) for public comment. The plan is required by the Oceans Act of 2008 to, among other things, be adaptive to evolving knowledge and understanding of the ocean environment. The plan’s Science Framework establishes a blueprint for future research and data acquisition and ensuring that the plan evolves and its management measures adapt to this new and enhanced information. As stated in Chapter 5 of the draft plan, an important part of the science framework is the development and implementation of a performance evaluation system with a series of indicators to help EEA and stakeholders evaluate the implementation of the Massachusetts Ocean Management Plan, identify the environmental and socio-economic impacts of plan management decisions, and identify new or emerging issues. Volume 2 of the draft plan contains a section entitled Development of Evaluation Measures for the Massachusetts Ocean Management Plan. This section outlines a proposed process “to identify measures of success or indicators that can be used to measure performance of management strategies in achieving desired outcomes.” As the development of indicators is a high priority of the draft plan, the Massachusetts Ocean Partnership (MOP) in consultation with EEA contracted with the Urban Harbors Institute (UHI) of the University of Massachusetts Boston (UMass Boston). The project team1 and other professionals from organizations and agencies experienced with the selection and use of indicators conducted the process outlined in Volume 2 of the draft plan to identify and select a set of environmental, socio-economic, and governmental indicators to evaluate the effectiveness of the Massachusetts Ocean Management Plan. The work described in this report also contributes to a broader interest and goal of the Massachusetts Ocean Partnership which is to coordinate indicator initiatives to inform ocean management and to advance the development and use of indicators of the ocean’s ability to provide ecosystem services. Currently, there are a number of initiatives, focusing on the coastal and ocean areas of the Northwest Atlantic/Gulf of Maine region, to develop indicators for various purposes and audiences. The process and products of this work in support of the Massachusetts Ocean Management Plan (e.g., the list of indicators and associated data) will be useful in collaborative efforts to integrate and coordinate these regional efforts

Understanding the peculiarities of the piezoelectric effect in macro-porous BaTiO₃

This work demonstrates the potential of porous BaTiO3 for piezoelectric sensor and energy-harvesting applications by manufacture of materials, detailed characterisation and application of new models. Ferroelectric macro-porous BaTiO3 ceramics for piezoelectric applications are manufactured for a range of relative densities, α = 0.30–0.95, using the burned out polymer spheres method. The piezoelectric activity and relevant parameters for specific applications are interpreted by developing two models: a model of a 3–0 composite and a ‘composite in composite’ model. The appropriate ranges of relative density for the application of these models to accurately predict piezoelectric properties are examined. The two models are extended to take into account the effect of 90° domain-wall mobility within ceramic grains on the piezoelectric coefficients $d_{3j}^{\ast}$. It is shown that porous ferroelectrics provide a novel route to form materials with large piezoelectric anisotropy $\left( {{{d_{33}^{\ast} } \mathord{\left/ {\vphantom {{d_{33}^{\ast} } {\left| {d_{31}^{\ast} } \right|}}} \right. \kern-0pt} {\left| {d_{31}^{\ast} } \right|}} > > 1} \right)$

Polynomial diffeomorphisms of C^2, IV: The measure of maximal entropy and laminar currents

This paper concerns the dynamics of polynomial automorphisms of ${\bf C}^2$. One can associate to such an automorphism two currents $\mu^\pm$ and the equilibrium measure $\mu=\mu^+\wedge\mu^-$. In this paper we study some geometric and dynamical properties of these objects. First, we characterize $\mu$ as the unique measure of maximal entropy. Then we show that the measure $\mu$ has a local product structure and that the currents $\mu^\pm$ have a laminar structure. This allows us to deduce information about periodic points and heteroclinic intersections. For example, we prove that the support of $\mu$ coincides with the closure of the set of saddle points. The methods used combine the pluripotential theory with the theory of non-uniformly hyperbolic dynamical systems

Error, reproducibility and sensitivity : a pipeline for data processing of Agilent oligonucleotide expression arrays

Background Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples. Results We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2% of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log2 units ( 6% of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators. Conclusions This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells