Biodiversity Informatics

Last chance to see? What is the role of SDI’s in the race to halt biodiversity Loss?

by Gregoire Dubois

Peedell, S., G. Dubois, A. Cottam, M. Schulz (2012). Last chance to see? – what is the role of SDI’s in the race to halt biodiversity loss? In: "Global Geospatial Conference 2012 - Spatially Enabling Government, Industry and Citizens", May 14-17, 2012, Québec City, Canada.

Attempts to stem the rate of biodiversity loss worldwide have so far failed to produce the desired outcomes. A new... more Attempts to stem the rate of biodiversity loss worldwide have so far failed to produce the desired outcomes. A new impetus to address this problem has been given at the culmination of the International Year of Biodiversity in 2010 with the Convention on Biodiversity (CBD) summit in Nagoya. Outcomes of the summit
include a Strategic Plan for Biodiversity 2011-2020 and the Aichi Biodiversity Targets. Global initiatives such as these generate many challenges for data gathering, sharing, analysis and presentation, and highlight the need for concerted action, including in the domain of spatial information. Are existing SDI’s providing the necessary data and technological platforms for the biodiversity community? The BIOPAMA (Biodiversity and Protected Areas Management) project, jointly run by the European Commission’s Joint Research Centre and the International Union for Nature Conservation (IUCN), is addressing this question as it seeks to establish regional observatories for biodiversity information in the Africa, Caribbean, Pacific (ACP) region. BIOPAMA will be a pioneer opportunity to implement tools such as the Digital Observatory of Protected Areas (DOPA), which have been the outcome of recent JRC research projects. Much like the subject matter they deal with, the IT environments of initiatives such as BIOPAMA and DOPA are extremely diverse “ecosystems”, with components that are highly interdependent on one another. Whilst the classic SDI paradigm does much to facilitate information exchange, and for which there are many operational examples, there is an ongoing need to rapidly develop highperformance, sophisticated architectures for distributed modeling and geoprocessing, which is pushing the boundaries of SDI and biodiversity informatics research. We will illustrate this through examples of our work on biodiversity monitoring across the globe.

Keywords: ACP, Protected Areas, Biodiversity, DOPA, BIOPAMA, GEO BON

Applications Of Natural Language Processing In Biodiversity Science

by Anne Thessen

in press for Advances in Bioinformatics

VertNet: A New Model for Biodiversity Data Sharing

by Carol Spencer

Biodiversity Soup: Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

by Douglas Yu

Douglas W. Yu, Yinqiu Ji, Brent C. Emerson, Xiaoyang Wang, Chengxi Ye, Chunyan Yang, Zhaoli Ding. 2012. Methods in Ecology and Evolution

1. Traditional biodiversity assessment is costly in time, money, and taxonomic expertise. Moreover, data are... more 1. Traditional biodiversity assessment is costly in time, money, and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution.

2. We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass-PCR amplification of the COI barcode gene, pyrosequencing, and bioinformatic analysis, which together we call ‘metabarcoding.’

3. We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent to metabarcoding.

4. Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and efficient measure of biodiversity.

Ecological niche modeling of customary medicinal plant species used by Australian Aborigines to identify species-rich and culturally valuable areas for conservation

by Jitendra Gaikwad

I am very thankful to Dr Peter Wilson (second-author) for helping and supervising me while conducting this study. Brainstorming sessions with him helped me to develop this idea, design the methodology, analyze the data and write the manuscript. Also thanks to my PhD supervisor (corresponding author) for providing me access to computational infrastructure

Customary medicinal plant species used by Australian Aborigines are disappearing rapidly with its associatedmore Customary medicinal plant species used by Australian Aborigines are disappearing rapidly with its associated
knowledge, due to the loss of habitats. Conservation and protection of these species is important as they represent sources of novel therapeutic phytochemical compounds and are culturally valuable. Information on the spatial distribution and use of customary medicinal plants is often inadequate and fragmented, posing limitations on the identification and conservation of species-rich areas and culturally valuable habitats.

In this study, the habitat suitability modeling program, MaxEnt, was used to predict the potential ecological niches of 431 customary medicinal plant species, based on bioclimatic variables. Specimen locality records were obtained from the Global Biodiversity Information Facility (GBIF) data portal and
from Australia’s Virtual Herbarium (AVH). Ecological niche models of 414 predicted species, which had 30 or more occurrence points, were used to produce maps indicating areas that were ecologically suitable for multiple species (concordance of high predicted ecological suitability) and having cultural values. For the concordance map, individual species niche models were thresholded and summed. To derive a map of culturally valuable areas, customary medicinal uses from Customary Medicinal Knowledgebase (CMKb) (www.biolinfo.org/cmkb) were used
to weight individual species models, resulting in a value within each grid cell reflecting its cultural worth.

Even though the available information is scarce and fragmented, our approach provides an opportunity to infer areas predicted to be suitable for multiple species (i.e. concordance hotspots) and to estimate the cultural value of a particular geographical area.

Our results also indicate that to conserve bio-cultural diversity, comprehensive information and active participation of Aboriginal communities is indispensable.

Building a biodiversity grid

by Alastair Culham

Andrew C. Jones, Richard J. White, W. A. Gray, Frank A. Bisby, Neil Caithness, Nick Pittas, Xuebiao Xu, Tim Sutton, N. J. Fiddian, Alastair Culham, Malcolm Scoble, Paul Williams, Oliver Bromley, Peter Brewer, Chris Yesson, Shonil Bhagwat

In the BiodiversityWorld project we are building a GRID to support scientific biodiversity-related research. The... more In the BiodiversityWorld project we are building a GRID to support scientific biodiversity-related research. The requirements as- sociated with such a GRID are somewhat different from other GRIDs, and this has influenced the architecture that we have developed. In this paper we outline these requirements, most notably the need to inter- operate over a diverse set of legacy databases and applications in an environment that supports effective resource discovery and use of these resources in complex workflows. Our architecture provides an invocation model that is usable over a wide range of resource types and underlying GRID middleware. However, there is a trade-off between the flexibility provided by our architecture and its performance. We discuss how this affects the inclusion of computationally intensive applications and appli- cations that are highly interactive; we also consider the broader issue of interoperation with other GRIDs.

DOPA, a Digital Observatory for Protected Areas Including Monitoring and Forecasting Services

by Gregoire Dubois

On the Contribution of Remote Sensing to DOPA, a Digital Observatory for Protected Areas

by Gregoire Dubois

Dubois, G., M. Clerici, J.F. Pekel, A. Brink, I. Palumbo, D. Gross, S. Peedell, D. Simonetti, M. Punga (2011). On the contribution of remote sensing to DOPA, a digital observatory from protected areas. In: "Proceedings of the 34th International Symposium on Remote Sensing of Environment", April 10-15, 2011, Sydney, Australia

The Digital Observatory for Protected Areas (DOPA) is a biodiversity information system currently developed as a set... more The Digital Observatory for Protected Areas (DOPA) is a biodiversity information system currently developed as a set of interoperable web services at the Joint Research Centre of the European Commission in collaboration with other international organizations, including GBIF, UNEP-WCMC, Birdlife International and RSPB. DOPA is not only designed to assess the state and pressure of Protected Areas (PAs) and to prioritize them accordingly, in order to support decision making and fund allocation processes, but it is also conceived as a monitoring and modeling service. To capture the dynamics of spatio-temporal changes in habitats and anthropogenic pressure on PAs, the automatic collection and processing of remote sensing data are processes at the heart of the system. In particular, DOPA uses information from EumetCAST and SpotVGT to compute environmental trends and detect anomalies every 10 days. Anthropogenic threats are also currently assessed through the analysis of agricultural pressure, population growth and habitat fragmentation around the protected areas. Fire activity in sub-Saharan protected areas which is derived from the MODIS fire products (active fires and burned areas) provide further support to park managers as well as to experts working for conservation and natural resource management. The purpose of this paper is to highlight the variety of uses of remote sensing data by the DOPA, the integration with other data sources, the practical implementation according to an architecture grounded in international initiatives such as GEOSS, GSDI and INSPIRE, and applications in monitoring and in ecological forecasting through e-Habitat, DOPAs' habitat modeling service.

eHabitat: a Contribution to the Model Web for Habitat Assessments and Ecological

by Gregoire Dubois

Dubois, G., J. Skoien, S. Peedell, J. De Jesus, G. Geller, A. Hartley (2011). eHabitat: a contribution to the model web for habitat assessments and ecological forecasting. In: Proceedings of the 34th International Symposium on Remote Sensing of Environment, April 10-15, 2011, Sydney, Australia

Abstract – In striving to improve the predictive capabilities of ecological forecasting we face three basic choices:... more Abstract – In striving to improve the predictive capabilities of ecological forecasting we face three basic choices: develop new models, improve existing ones or increase the connectivity of models so they can work together. The latter approach of chaining different interoperable models is of particular interest, as technical developments have made it increasingly viable to combine models that can answer more questions than the individual models alone, allowing users to address complex questions, often of a multi-disciplinary nature. This concept of a Model Web encourages the setting up of a dynamic network of interoperating models, communicating with each other using standardized web services. It is the purpose of this paper to introduce the potential contribution of eHabitat to the Model Web. eHabitat is conceived as a Web Processing Service for computing the likelihood of finding ecosystems with equal properties. By developing eHabitat according to Model Web principles, end-users can define the thematic layers for input to the model from various sources. These input layers are discovered using standards-based catalogues, which are a fundamental component of Model Web and generic Spatial Data Infrastructures. eHabitat integrates data ranging from remote sensing data to socio-economical indicators, thus offering a huge potential for multi-disciplinary modelling.

Towards an interoperable web service for the monitoring of African protected areas.

by Gregoire Dubois

In: Proceedings of the 33rd International Symposium on Remote Sensing of Environment (ISRSE)”, May 4-8, 2009 Stresa, Italy

The Assessment of African Protected Areas web site is an online information system based on satellite technology... more The Assessment of African Protected Areas web site is an online information system based on satellite technology allowing decision makers to assess the state of 741 protected areas in Africa and to prioritize them according to biodiversity values and threats when allocating funds. The current architecture of the system and the large variety of data types and sources involved here render uneasy the maintenance and potential developments of the web site. Future improvements and innovations of the system depend thus largely on its evolution towards an interoperable web service able to exchange a large variety of data coming from different sources. We discuss here how the current system can become an element of the Shared Environmental Information System (SEIS) by adopting a Service Oriented Architecture with model servers that can provide analysis tools for ecological forecasting as proposed in Model Web.

Geoinformatics for the Environmental Surveillance of Protected Areas in Africa

by Gregoire Dubois

Nelson, A., A. Hartley, G. Dubois, M. Punga (2009) Geoinformatics for the Environmental Surveillance of Protected Areas in Africa. In: “Proceedings of the StatGIS09: GeoInformatics for Environmental Surveillance ”, June 17-19, 2009 Milos, Greece

The African Protected Areas Assessment Tool (APAAT) is an online information system developed for decision makers to... more The African Protected Areas Assessment Tool (APAAT) is an online information system developed for decision makers to help them as-sess the state of 741 protected areas in Africa and prioritize them according to biodiversity values and threats when allocating funds. Largely based on satellite technology, the system has also been developed as an experimental early warning system for detecting environmental anomalies in the pro-tected areas. Every ten days (dekads) fire activity, vegetation growth, vege-tation water content, the percentage of water bodies and rainfall are auto-matically compared against seasonal norms and alerts can be issued. In ad-dition to this short term monitoring activity, a longer term approach is fore-seen which will allow the monitoring and possibly the forecasting of the impact of the main threats to biodiversity, namely habitat degradation and climate change.

Continental-Scale Patterns In Benthic Invertebrate Diversity: Insights From the MacroBen Database

by Ioannis Karakassis

Biological Geography of the European Seas: Results From the MacroBen Database

by Ioannis Karakassis

How Diverse is Aquatic Biodiversity Research?

by Ioannis Karakassis

Recovery from the most profound mass extinction of all time

by Sarda Sahney

Sahney, S. and M.J. Benton 2008. Recovery from the most profound mass extinction of all time. Proceedings of The Royal Society of London. Series B, Biological Sciences 275:759-765.

The end-Permian mass extinction, 251 million years (Myr) ago, was the most devastating ecological event of all time,... more The end-Permian mass extinction, 251 million years (Myr) ago, was the most devastating ecological event of all time, and it was exacerbated by two earlier events at the beginning and end of the Guadalupian, 270 and 260 Myr ago. Ecosystems were destroyed worldwide, communities were restructured and organisms were left struggling to recover. Disaster taxa, such as Lystrosaurus, insinuated themselves into almost every corner of the sparsely populated landscape in the earliest Triassic, and a quick taxonomic recovery apparently occurred on a global scale. However, close study of ecosystem evolution shows that true ecological recovery was slower. After the end-Guadalupian event, faunas began rebuilding complex trophic structures and refilling guilds, but were hit again by the end-Permian event. Taxonomic diversity at the alpha (community) level did not recover to pre-extinction levels; it reached only a low plateau after each pulse and continued low into the Late Triassic. Our data showed that though there was an initial rise in cosmopolitanism after the extinction pulses, large drops subsequently occurred and, counter-intuitively, a surprisingly low level of cosmopolitanism was sustained through the Early and Middle Triassic.

Links between global taxonomic diversity, ecological diversity and the expansion of vertebrates on land

by Sarda Sahney

Sahney, S., Benton, M.J. and Paul A. Ferry 2010. Links between global taxonomic diversity, ecological diversity and the expansion of vertebrates on land. Biology Letters. 6:544-547

Tetrapod biodiversity today is great; over the past 400 Myr since vertebrates moved onto land, global tetrapod... more Tetrapod biodiversity today is great; over the past 400 Myr since vertebrates moved onto land, global tetrapod diversity has risen exponentially, punctuated by losses during major extinctions. There are links between the total global diversity of tetrapods and the diversity of their ecological roles, yet no one fully understands the interplay of these two aspects of biodiversity and a numerical analysis of this relationship has not so far been undertaken. Here we show that the global taxonomic and ecological diversity of tetrapods are closely linked. Throughout geological time, patterns of global diversity of tetrapod families show 97 per cent correlation with ecological modes. Global taxonomic and ecological diversity of this group correlates closely with the dominant classes of tetrapods (amphibians in the Palaeozoic, reptiles in the Mesozoic, birds and mammals in the Cenozoic). These groups have driven ecological diversity by expansion and contraction of occupied ecospace, rather than by direct competition within existing ecospace and each group has used ecospace at a greater rate than their predecessors.

Rainforest collapse triggered Pennsylvanian tetrapod diversification in Euramerica

by Sarda Sahney

Sahney, S., Benton, M.J. & Falcon-Lang, H.J. 2010 Rainforest collapse triggered Pennsylvanian tetrapod diversification in Euramerica. Geology. 38: 1079-1082.

Abrupt collapse of the tropical rainforest biome (Coal Forests) drove rapid diversification of Carboniferous tetrapods... more Abrupt collapse of the tropical rainforest biome (Coal Forests) drove rapid diversification of Carboniferous tetrapods (amphibians and reptiles) in Euramerica. This finding is based on analysis of global and alpha diversity databases in a precise geologic context. From Visean to Moscovian time, both diversity measures steadily increased, but following rainforest collapse in earliest Kasimovian time (ca. 305 Ma), tetrapod extinction rate peaked, alpha diversity imploded, and endemism developed for the first time. Analysis of ecological diversity shows that rainforest collapse was also accompanied by acquisition of new feeding strategies (predators, herbivores), consistent with tetrapod adaptation to the effects of habitat fragmentation and resource restriction. Effects on amphibians were particularly devastating, while amniotes ('reptiles') fared better, being ecologically adapted to the drier conditions that followed. Our results demonstrate, for the first time, that Coal Forest fragmentation influenced profoundly the ecology and evolution of terrestrial fauna in tropical Euramerica, and illustrate the tight coupling that existed between vegetation, climate, and trophic webs.