Categorization of species as native or nonnative using DNA sequence signatures without a complete reference library.

New genetic diagnostic approaches have greatly aided efforts to document global biodiversity and improve biosecurity. This is especially true for organismal groups in which species diversity has been underestimated historically due to difficulties associated with sampling, the lack of clear morphological characteristics, and/or limited availability of taxonomic expertise. Among these methods, DNA sequence barcoding (also known as "DNA barcoding") and by extension, meta-barcoding for biological communities, has emerged as one of the most frequently utilized methods for DNA-based species identifications. Unfortunately, the use of DNA barcoding is limited by the availability of complete reference libraries (i.e., a collection of DNA sequences from morphologically identified species), and by the fact that the vast majority of species do not have sequences present in reference databases. Such conditions are critical especially in tropical locations that are simultaneously biodiversity rich and suffer from a lack of exploration and DNA characterization by trained taxonomic specialists. To facilitate efforts to document biodiversity in regions lacking complete reference libraries, we developed a novel statistical approach that categorizes unidentified species as being either likely native or likely nonnative based solely on measures of nucleotide diversity. We demonstrate the utility of this approach by categorizing a large sample of specimens of terrestrial insects and spiders (collected as part of the Moorea BioCode project) using a generalized linear mixed model (GLMM). Using a training data set of known endemic (n = 45) and known introduced species (n = 102), we then estimated the likely native/nonnative status for 4,663 specimens representing an estimated 1,288 species (412 identified species), including both those specimens that were either unidentified or whose endemic/introduced status was uncertain. Using this approach, we were able to increase the number of categorized specimens by a factor of 4.4 (from 794 to 3,497), and the number of categorized species by a factor of 4.8 from (147 to 707) at a rate much greater than chance (77.6% accuracy). The study identifies phylogenetic signatures of both native and nonnative species and suggests several practical applications for this approach including monitoring biodiversity and facilitating biosecurity

The cultural, ethnic and linguistic classification of populations and neighbourhoods using personal names

There are growing needs to understand the nature and detailed composition of ethnicgroups in today?s increasingly multicultural societies. Ethnicity classifications areoften hotly contested, but still greater problems arise from the quality and availabilityof classifications, with knock on consequences for our ability meaningfully tosubdivide populations. Name analysis and classification has been proposed as oneefficient method of achieving such subdivisions in the absence of ethnicity data, andmay be especially pertinent to public health and demographic applications. However,previous approaches to name analysis have been designed to identify one or a smallnumber of ethnic minorities, and not complete populations.This working paper presents a new methodology to classify the UK population andneighbourhoods into groups of common origin using surnames and forenames. Itproposes a new ontology of ethnicity that combines some of its multidimensionalfacets; language, religion, geographical region, and culture. It uses data collected atvery fine temporal and spatial scales, and made available, subject to safeguards, at thelevel of the individual. Such individuals are classified into 185 independentlyassigned categories of Cultural Ethnic and Linguistic (CEL) groups, based on theprobable origins of names. We include a justification for the need of classifyingethnicity, a proposed CEL taxonomy, a description of how the CEL classification wasbuilt and applied, a preliminary external validation, and some examples of current andpotential applications

Defining interoperability standards: A case study of public health observatory websites

The Association of Public Health Observatories (APHO) is a group of region-based health-information providers. Each PHO publishes health-related data for their specific region. Each observatory has taken a national lead in one or more key health area - such as 'cancer' or Obesity'. In 2003, a project was initiated to develop 'interoperability' between public health observatory websites, so the national resources published by one lead observatory could be found on the websites for each other PHO. The APHO interoperability project defined a set of requirements for each PHO - websites should comply with the current government data standards and provide webservices to allow data to be searched in real-time between different PHOs. This thesis describes the production of an interoperable website for the North East Public Health Observatory (NEPHO) and the problems faced during implementation to comply with the APHO interoperability requirements. The areas of interoperability, e-Government and metadata were investigated specifically in suitability for NEPHO and an action list of tasks necessary to achieve the project aims was drawn up. This project has resulted in the successful introduction of a new NEPHO website that complies with the APHO and e-Govemment requirements, however interoperability with other organisations has been difficult to achieve. This thesis describes how other organisations approached the same APHO interoperability criteria and questions whether the national project governance could be improved

Data Driven Discovery in Astrophysics

We review some aspects of the current state of data-intensive astronomy, its methods, and some outstanding data analysis challenges. Astronomy is at the forefront of "big data" science, with exponentially growing data volumes and data rates, and an ever-increasing complexity, now entering the Petascale regime. Telescopes and observatories from both ground and space, covering a full range of wavelengths, feed the data via processing pipelines into dedicated archives, where they can be accessed for scientific analysis. Most of the large archives are connected through the Virtual Observatory framework, that provides interoperability standards and services, and effectively constitutes a global data grid of astronomy. Making discoveries in this overabundance of data requires applications of novel, machine learning tools. We describe some of the recent examples of such applications.Comment: Keynote talk in the proceedings of ESA-ESRIN Conference: Big Data from Space 2014, Frascati, Italy, November 12-14, 2014, 8 pages, 2 figure

Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures

Deep-sea ecosystems are reservoirs of biodiversity that are largely unexplored, but their exploration and biodiscovery are becoming a reality thanks to biotechnological advances (e.g., omics technologies) and their integration in an expanding network of marine infrastructures for the exploration of the seas, such as cabled observatories. While still in its infancy, the application of environmental DNA (eDNA) metabarcoding approaches is revolutionizing marine biodiversity monitoring capability. Indeed, the analysis of eDNA in conjunction with the collection of multidisciplinary optoacoustic and environmental data, can provide a more comprehensive monitoring of deep-sea biodiversity. Here, we describe the potential for acquiring eDNA as a core component for the expanding ecological monitoring capabilities through cabled observatories and their docked Internet Operated Vehicles (IOVs), such as crawlers. Furthermore, we provide a critical overview of four areas of development: (i) Integrating eDNA with optoacoustic imaging; (ii) Development of eDNA repositories and cross-linking with other biodiversity databases; (iii) Artificial Intelligence for eDNA analyses and integration with imaging data; and (iv) Benefits of eDNA augmented observatories for the conservation and sustainable management of deep-sea biodiversity. Finally, we discuss the technical limitations and recommendations for future eDNA monitoring of the deep-sea. It is hoped that this review will frame the future direction of an exciting journey of biodiscovery in remote and yet vulnerable areas of our planet, with the overall aim to understand deep-sea biodiversity and hence manage and protect vital marine resources

Marine biodiversity: A science roadmap for Europe

In the past ten years, Europe has made significant progress in marine biodiversity research and knowledge generation owing to strong support, funding, and coordination of research effort. However, there is still a major knowledge deficit and many of the important programmes and initiatives which have driven this progress have now ended. While biodiversity policy has also advanced, Europe has failed to achieve the biodiversity targets it has set itself. To meet these targets, effective science-based decisions and management will be necessary. This requires good science, strong European research collaboration, enhanced observing and research capacities, and effective science-policy interfaces