There has been a great deal of discussion surrounding the outcomes of the recent Rio+20 Earth Summit. In this guest post, Will Bibby asks if there was anything in the conference commitments for freshwater biodiversity or it was little more than just one big talkfest.
There were no new agreements, no bold targets. In fact, there was very little in the way of concrete proposals at all. The conference was essentially a reaffirmation of the UN’s commitment to the principles of sustainable development established at the first Earth Summit 20 years ago. There were a few tweaks and some re-branding along the way, but all in all the draft conference document was painfully unambitious. That being said, it’s not all doom and gloom: over 700 voluntary commitments were signed by governments, NGOs and companies. Collectively, these commitments mobilize over $500 billion in actions towards sustainable development. Unfortunately, only a small handful of these commitments offer anything for freshwater biodiversity.
Photo Credit: Aliencrow, 21 June 2012, Wikimedia Commons
Though not one of the ‘critical issues’ listed above, biodiversity conservation received a reasonable amount of coverage during the conference. One of the principles of the ‘green economy’, for example, is to protect and restore biodiversity and natural habitats as integral to development and human well-being, and develop a system of governance that protects the resilience of ecosystems to prevent irreversible damage. One concrete voluntary commitment was to provide the International Union for the Conservation of Nature (IUCN) with an extra $120 million to improve the conservation status of species and ecosystems. Another development was the announcement that the Global Environment Facility (GEF) would be expanding its scope to include a broader range of concerns and fund more projects that protect biodiversity. In general, however, the focus was largely on terrestrial (particularly forest) and marine biodiversity, with freshwater biodiversity conservation receiving few explicit mentions in official documents.
The two most significant commitments to come out of Rio+20 for freshwater biodiversity are efforts to generate a better understanding of the ecosystem service value of water and wetlands and a project to harmonise global biodiversity modelling, called the HarmBio partnership.
The first of these commitments aims to build global capacity on using the Economics of Ecosystems and Biodiversity (TEEB) approach for water and wetlands policy and decision-making. Led by the Ramsar Convention of Wetlands in partnership with the CBD, UNEP, IUCN, among others, its goal is to encourage policy momentum and business commitment for the conservation, investment in, and wise use of freshwater and wetland ecosystems5.
The main objective of the HarmBio partnership is the harmonization of current models and datasets of terrestrial, freshwater and marine biodiversity to improve the reliability of future projections of biodiversity change under various policy options and so enable improved environmental decision-making6. It aims to address the problem that there are neither agreed metrics of biodiversity produced as standard outputs from models, nor are there common datasets used for calibration and validation by modelling efforts – an issue that aligns with the aims of the BioFresh project!
In short, the HarmBio project and TEEB approach to freshwater and wetlands policy-making represent the most promising commitments to emerge from the summit, and the increased funding for the IUCN and scope of the GEF may have some ‘downstream’ effects for freshwater biodiversity conservation. All in all though, freshwater biodiversity barely got a look in at Rio+ 20. This once again underlines again the challenge of raising the policy profile of freshwater biodiversity.
Documents cited
UNCSD 2012, ‘Rio+20 Voluntary Commitments’, .
2 Stoddart H., Riddlestone S. & Vilela M. 2012, ‘Principles for the Green Economy’.
3 UNCSD 2012, ‘Valuing and conserving nature for a sustainable future’
6 UNCSD 2012, ‘Harmonizing Global Biodiversity Modelling (HarmBio)’
What is a Digital Object Identifyer?
A guiding principle of science is that we never use another’s work without giving appropriate citation. The developments in data publishing profiled in this blog series are a consequence of web and computing technologies: effective data-sharing therefore requires a means to cite objects that exist in the digital medium. Digital objects – documents, images, data files etc.- are in effect ‘housed’ and an internet address (url)> However, their location on a web-site may be moved and internet addresses are constantly being closed down, changed, or created. To address this challenge, and the need for a citation format that aligns with the ‘cut and paste’ and ‘click and link’ practicse of the internet, the Association of American Publishers and the Corporation for National Research Initiatives conceived the DOI system.
The idea is elegantly simple. An organization – e.g. the International DOI Foundation – manages a central repository (or dorepository). Owners register their digital objects on the directory using a globally available system of character strings (the object ‘handle’ or “digital identifier”). This DOI is a permanent whereas its internet address and other data associated with the object may change. The handle system (basically software protocol that underlie the operation of the internet) is used to resolve ‘handles’ into the “information necessary to locate, access, contact, authenticate, or otherwise make use of digital resources”. Lastly, a Digital Object Registry (or doregistry) is used to define collections of digital objects that exist in multiple repositories to support browsing and searching.
A more detailed overview on this architecture is available on the International DOI Foundation web-site and in a paper by Robert Kahn & Robert Wilensky that describes in detail the conceptual and technical design.
When you start paying attention to DOI’s you will see them everywhere. The one attached to this figure, reproduced from an important paper by Carol Tenopir on scientific practices and perceptions regarding data-sharing, illustrates how the character string is constructed. This DOI could be read as “doi: address of directory where object is logged/journal. PLoS One. ISBN number. the specific part of the journal where the object is located” Pasting the DOI into the web-service dx.doi.org or prefixing a DOI with this url e.g http://dx.doi.org/10.1371/journal.pone.0021101.g001 will take you to the document. Alternatively you pasting a DOI into most web-browsers will take you to the document via a search engine.
Increasingly, scientists publishing data via portals such as GBIF and BioFresh are attaching a DOI to their data sets. Organizations such as DataCite, formed to support data publishing, sharing and archiving provide services to ‘mint’ DOIs for data. However, many larger universities and research institutes are establishing digital research & data archives and the ability to ‘mint’ dois for their scientists is an integral part of such initiatives.
We hope this explanation captures the essence of Digital Object Identifiers and we would welcome comments to help clarify or expand upon key points.
Paul Jepson & Aaike De Wever
Citations
Kahn, R & R. Wilensky (2008) A framework for distributed digital object services. International Journal on Digital Libraries (2006) 6: 115–123 DOI 10.1007/s00799-005-0128-x
Tenopir, C. et al (2011) Data Sharing by Scientists: Practices and Perceptions. PLoS ONE 6(6): e21101. doi:10.1371/journal.pone.0021101
Science made easier : Darwin Core explained
A key barrier to data publishing – making data available for others to use – is the simple reality that most people have devised their own terms and labels to order their data sets. Wouldn’t life be easy for those creating, managing and using data portals if we all used the same set of terms to describe our data? This is the purpose of the Darwin Core Standard, a seriously useful and authoritative output of the Taxonomic Database Working Group (TDWG) of the International Union of Biological Scientists.
The Darwin Core is set to become the ‘industry standard’ for the field of Biodiversity informatics. It comprises a list of terms and technical descriptions relating to attributes of species and distributional data. The latest version is comprehensive and arises from an iterative process started in 2009 and guided by the principle of “keeping the standard as simple and open as possible and to develop terms only when there is shared demand”. Adopting the standard not only means that data can be upload into important biodiversity data portals such as GBIF and BioFresh, but it also provides an invaluable prompt when designing new databases. John Wieczorek and colleagues have published an excellent overview of both the standard and its applications in PLoS One, and full details of the technical aspects are available from the TDWG web-site.
However, if you are just looking for a quick introduction we suggest you check out the two videos below. In the first, two robots in bar talk about the principles of the Darwin Core (like Robots would!)..
and in the second David Remsen helpfully walks viewers through the Darwin Core Archive Assistant which is an on-line tool to assist in the publication of biodiversity data.
Citation: Wieczorek J, Bloom D, Guralnick R, Blum S, Döring M, et al. (2012) Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. PLoS ONE 7(1): e29715. doi:10.1371/journal.pone.0029715
What does a Data paper look like?
Making datasets discoverable through the metadatabase and publishing them on-line is one of the main aims of the BioFresh project. Pensoft Publishers recently started calling for data papers based on primary biodiversity datasets published to GBIF (Penev et al. 2011). BioFresh partners have several in preparation and the practice of publishing data papers seems set to become normal practice.
So what is a ‘metadata paper’ or ‘database paper’? Well as the terms suggest it is a paper that focuses on the description of a database. Such papers could be conceived as either a pure description of the dataset for publication in a specialized journal or as a more extensive scientific article giving a broader insight in the database which might be targeted at a regular scientific journal. A “pure” data paper might be limited to an abstract published in a scientific journal together with descriptive and technical metadata. In such cases the actual data files would be made available on-line, as is the case of the papers in the Ecological Society of America’s Ecological archive, or via data portals such as GBIF. However, it is expected that in addition to describing the data content, data papers will include sections summarizing the history of the data set (e.g. original purpose, mode and time of generation, funding body etc.) and its perceived value and usefulness to scientific research (fundamental and/or applied). (see two examples below).
If you want to get into data publishing, and we encourage you to do so, nice examples of data papers are by Jones et al (2009) on mammals and Brose etal (2005) on body sizes. Pensoft Publishing has produced useful data publishing policies and guidelines and GBIFs integrated publishing tool (IPT) offers a facility to generate a draft paper outline containing the metadata information of the dataset. BioFresh is currently adding similar export functions to the BioFresh metadatabase.
Example Data Papers
Jones et al. (2009). PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. (W. K. Michener, Ed.) Ecology, Ecological Archives E090-184, 90(9), 2648–2648. Ecological Society of America.
Brose et al. (2005). Body sizes of consumers and their resources. Ecology 86:2545.
Penev, L., Mietchen, D., Chavan, V., & Hagedorn, G. (2011). Pensoft Data Publishing Policies
The latest issue of BioScience carries a viewpoint letter from the Biofresh data management ‘team’ announcing an exciting new initiative to encourage the publication of the data analyzed and reported in scientific papers. As a result of Biofresh efforts, 17 journals publishing on Freshwater Biodiversity have agreed to include in their guidelines for authors the statement that “Authors are encouraged to place all species distribution records in a publicly accessible database such as the national Global Biodiversity Information Facility (GBIF) nodes or data centers endorsed by GBIF, including BioFresh“.
Lead author Aaike De Wever, data manager of the Biofresh project explains the significance and origins of this initiative:
“One of the major goals of BioFresh is to make freshwater biodiversity data open and freely available. This will allow broader-scale analyses that will open new frontiers in freshwater science to support enhanced freshwater biodiversity policy and management. As data publishing practices are not yet well established in the freshwater community, we are trying to convince scientists to make their data available through various means. This includes the promotion of data papers, and engaging with funding agencies and scientific journals to encourage data publication.
Last year, during the Seventh Symposium for European Freshwater Science (SEFS7) in Girona, we had the opportunity to convene editors from 12 scientific freshwater journals to explore their role in biodiversity data mobilization. During this meeting we stressed the need to bring primary biodiversity data on where, when, how and by whom species have been observed or collected available to other scientists and discussed the role of journals to encourage data publication or submission. Subsequently editors and publishers of the represented journals as well as a number of additional journals approved inclusion of a statement in their author guidelines (above) encouraging data publication”.
The participating journals are Aquatic Botany, Aquatic Conservation: Marine and Freshwater Ecosystems, Aquatic Ecology, Aquatic Sciences, Ecology of Freshwater Fish, Freshwater Biology, Freshwater Reviews, Fundamental and Applied Limnology, Hydrobiologia, Inland Waters, International Review of Hydrobiology, Freshwater Science (formerly, Journal of the North American Benthological Society), Journal of Fish Biology, Journal of Limnology, Journal of Plankton Research, Limnetica, Limnologica, Marine and Freshwater Research, and River Systems.
In contrast to other initiatives on making data publicly available, BioFresh is specifically targeting primary biodiversity data, which is limited to a standard set of fields, much like the format of GenBank, allowing direct integration in large-scale datasets. Detailed instructions on how to submit data can be found at this link.
Since the early 1990s scientists have been working to enhance the impact and efficiency of site-based conservation approaches. The field of systematic conservation Planning (1) is guided by the so-called ‘representation principle’, an influential policy goal formulated by IUCN ecologist Raymond Dasman in 1972 (2) and simply stated as “The creation of world-wide network of natural reserves that encompass within their boundaries the variety of species and habitats found on earth”. Initially the scientific focus was on developing principles and tools to optimize reserve network design assuming a largely static biota (e.g. the MARXAN conservation planning software). The new scientific frontier in conservation planning is about taking into account the changes in species distribution and occurrence in response to climate and other environmental change. This is so that ‘long-term persistence’ can be incorporated into reserve system design. Needless to say conservation planning for freshwater biodiversity under changing environmental conditions is particularly challenging given the fluid and dynamic nature of freshwater systems!
Writing in the May issue of Global Ecology and Biogeography, BioFresh team member Clément Tisseuil and colleagues add a significant new dimension to our ability to predict how assemblies of fish species (termed beta diversity) will change in time and space in response to climate change. They applied two concepts in biogeography to explore and project the future distributions of 18 fish species for the 2010-2100 period based on data from 50 sites in the Adour-Garone River Basin in France.
The Tarn River France by By Thomas Rosenau [CC-BY-SA-2.5 (http://creativecommons.org/licenses/by-sa/2.5)%5D
The first concept of species turn-over seeks to understand how some species may be replaced by others under different scenarios. The second, and slightly more difficult concept of nestedness, refers to how an ecological system is organized. So for instance, we might prioritize a site for conservation based on the richness of the species assembly (Alpha diversity), however it is vital to know the extent to which other less species rich sites contain sub-sets of the species of the rich sites (degree of nestedness). The concept of nestedness thus enables scientists to identify the processes that lead to species loss or gain in sites .
The significance of this new study is that it is the first to take nestedness fully into account when projecting changes (differences) in fish assemblages at different places and at different times along a river gradient .
Commenting on the significance of the research Clement Tisseuil notes “We showed that the composition of local fish assemblages will greatly change over the 21st century, but this is consistent with previous studies of fish faunas. Our contribution is to distinguish between the turnover and nested components of fish diversity and how these shape the processes that lead to changes in fish species assemblies over time and space. Our key finding was that changes in species composition projected in upstream and downstream sites were mainly caused by differences in species richness among nested fish assemblages, whereas those projected in midstream sites were almost entirely caused by a process of species turnover ”
Literature:
Tisseuil1, C., Leprieur, F., Grenouillet, G., Vrac, M & S. Lek (2012) Projected impacts of climate change on spatio-temporal patterns of freshwater fish beta diversity: a deconstructing
approach Global Biogeography and Ecology: 773
(1) Margules, C.R.& R. L. Pressey (2000) Systematic Conservation Planning. Nature, 405, 243-253.
(2) Dasmann, R.F. (1972) Towards a system for classifying natural regions of the world and their representation by national parks and reserves. Biological Conservation, 4, 247-255.
A reality of 21st century science is that publications and citations are key metrics used to evaluate the performance and impact of scientists. Until recently, there has been no incentive for work -pressured scientists (other than good will) to invest time in preparing their data sets so they can be shared and used by others. With the launch of journals specializing in the publication of data papers this looks set to change. Data papers, can perhaps be compared to those reporting a new taxon: they will have a standard format and users of the data set will cite the data paper in a similar manner to how scientists cite the authority (descriptor paper) when using a scientific name. In this way, scientists contributing data to the common scientific endeavor will gain a publication credit and the number of citations will provide a measure of the scientific value of the data.
Lyubomir Penev of Pensoft Publishers has launched several innovative journals in biodiversity science, including an established infrastructure for publishing and dissemination of biodiversity data, and he kindly provided the following perspectives on the value and importance of data journals.
Biofresh Blog: What motivated you to launch a family of innovative journals for the publication and dissemination of biodiversity information?
Lyubomir Penev: The main motivation is perhaps that, as a biodiversity scientist, I have often been disappointed with the speed and manner with which conventional journals handle manuscripts and data. I was even more disappointed with the dissemination of published results, which are often hidden behind a pay-wall barrier with restrictions for copyright and use. Our journals build on three important pillars, namely open access, high-tech XML-based editorial workflow, and active dissemination of the results we publish for our authors.
BB: Why do you think scientists should make the effort to submit data papers: what’s in it for them?
LP: There are many benefits here and they are certainly not restricted to the authors of data papers alone. First, data collectors, managers and authors will be properly credited through a permanent scientific record, priority registration and citation of the data paper. Second, the extended metadata associated with a data set will be properly described and published in order to make data easy to share, use and re-use for others scientists. Sharing data will open new perspectives for collaboration with other scientific groups and institution. Last but not least, re-use of original and collated data sets will tremendously increase the efficiency of public funds investments in gathering all these data!
BB: To what extent do you think data journals will change the way we do Science?
LP: The change will be dramatic and extremely useful in my opinion. The appearance of new data visualization and analysing tools will lead to an ever increasing interest in inter-operability and collation of data with compatible data gathered by other groups. This should provide exciting new views and produce better proven scientific results.
The titles of journals in the Pensoft family include ZooKeys (systematic zoology, phylogeny and biogeography), PhytoKeys (systematic botany), NeoBiota (alien species), and Nature Conservation. A similar initiative is Dataset Papers in Ecology.
Saving Biodiversity Data
With the strap-line ‘Biodiversity Needs Data’, reBIND is a fantastic new initiative of the Botanic Gardens and Museum in Berlin funded by the German Research Foundation (DFG) that responds to the reality that many scientists collate valuable biodiversity datasets which are then stored on their personal hard-drives or archived on media which become out of date (remember Zip drives!). As a result, important ‘legacy’ data sets are being lost, or at risk of being lost, as scientists retire, change office or clear out their lofts.
The aim of reBIND is simple: to provide the tools to integrate isolated databases into an institutional data curation strategy. To this end, the reBIND team is developing workflows that combine software tools for transforming data stored in outdated database systems into well-documented, standardized, and commonly understood XML-formats with a system for storing, documenting, and publishing the information as a web service.
It’s a neat idea and wonderfully explained in this innovative and engaging video.
Knowledge on the status and distribution of biodiversity is fundamental both to the delivery of key conservation conventions and the development of effective policy planning and management. Unfortunately the temporal and spatial resolution of available biodiversity data currently falls well short of what is needed. This data shortfall is constraining the ability of conservation science and management to effectively embrace important concepts of adaptive management, subsidiarity, participation as well as big new policy frames such as the ecosystem approach.
BioFresh is part of a wider scientific endeavor working to improve geographic databases on the distribution of biodiversity on Earth. This involves creating a new digital architecture of data platforms and portals to pull together and make accessible biodiversity data-sets languishing on servers in research institutes and on the hard-drives of people’s personal computers. Needless to say achieving this vision is not exactly a walk in the park! In an earlier Special Feature on Assembling the Freshwater Database, BioFresh scientist, Aaike De Wever introduced the challenges involved in setting up a system of interoperable databases and explained some key terminology: metadata, inter-calibration and so forth. In this special feature we continue this theme by presenting an overview of some important, and we think exciting, advances in data publication.
Over the next 3 weeks we will run the following series of posts reporting on important new developments, new projects, and explaining terms. If you think there are other important aspects of data publishing that we should cover please let us know. We also invite you to add your comments to amplify and extend each post so as to make this special feature as useful as possible.
We hope that you will find this special feature interesting and would be grateful if you could let your colleagues and students know if its existence.
Paul Jepson & Aaike De Wever
Posts:
Saving Biodiversity Data, an introduction to the ReBIND project.
The Arrival of Data Journals including and interview with Lyubomir Penev of Pensoft Publishers.
Freshwater Journals Unite to Boost Primary Biodiversity Data Publication reports an important new agreement on data publishing.
What does a Data paper look like? outlines the structure and content of a typical data paper
Science made easier : Darwin Core explained introduces this important standard which is helping overcome key barriers to data publishing.
What is a digital object identifier? explores how this can be applied to data sets.
The effect of dams on fish biodiversity: A global view.
A salmon jumping up a waterfall in Canada. Diadramous fish species often face mortality or reproductive failure when their migratory route is obstructed by dams. Image: Jerome Charaoui.
The world is currently facing a freshwater biodiversity crisis and the key to preventing further extinction lies in understanding all the threats facing aquatic habitats. Global freshwater habitats are losing biodiversity faster than terrestrial or marine areas, but so far they are the least well understood. Amongst the threats to freshwater species, including climate change and pollution, the most difficult to quantify are man-made obstructions to water flow. Dams can be found in every major biosphere, but very little is known about the effect of river obstruction on freshwater biodiversity, especially on a global scale.
Damming a river has a variety of effects on the freshwater ecosystem, more than just altering the flow from A to B. Dams create calm bodies of water, changing overall temperature regimes and sediment transport, leading to conditions which tend to favour generalist species. Loss of specialist species, particularly endemics, changes the community structure and leads to biotic homogenization. A dam will withhold sediment in the reservoir, not just decreasing the amount of substrate available to local freshwater species, but even impacting diadromous, estuarine and marine species much further downstream. The competition between resident species for food and breeding sites will increase as damming isolates populations, and perhaps more importantly, damming completely restricts migratory fish species. Isolation may lead to decreases in genetic diversity and therefore puts species at greater risk from disease. All of these effects may be exacerbated by changes in the surrounding land use. Overall, damming river flow will lead to both a loss of native species, but also an increase in exotic species which are more likely to become established in degraded habitats. For this reason, dams are one of the greatest global threats to freshwater biodiversity.
A lack of data on global freshwater fish distributions has restricted a thorough investigation of the dam-related threats to fish species. However, a recent publication by Liermann et al maps global dam obstruction, identifying areas and taxa at risk of species loss. This is the first paper to quantify this in a manner which could be useful for future planning and management. Liermann et al quantify and map dam obstruction in all of the world’s main freshwater ecoregions (397). These are areas that contain geographically distinct groups of freshwater communities. This data was integrated with fish distribution data, particularly focussing on the numbers of obligate diadromous species (species demonstrating migratory behaviour between freshwater and marine habitats, such as the Salmonids) and ecoregional endemics. These species were used as a measure of potential species loss in relation to dam obstruction. The model also included an assessment of the difference between dam impact in an undisturbed landscape and the compounded effect of dams and land-use change. The distribution of areas predicted to be most affected by climate change were also compared with the distribution of the most heavily obstructed ecoregions.
Liermann et al produce the first comprehensive set of maps for highlighting habitat fragmentation by dam obstruction and the corresponding taxa and ecoregions most at risk of species loss. This information is vital for providing information needed to identify the freshwater systems most in need of protection. 18 ecoregions were identified for which less than 50% of the freshwater systems were free flowing. These areas include central and southern Iberia, the Mississippi, the Indus Basin, and the Murray Darling. Some of these areas also face high levels of landscape alteration. Liermann et al identify 8 ecoregions which may be facing the highest level of threats to species loss, but would therefore benefit the most from conservation and restoration projects. These ecoregions also have a high number of endemic and diadromous species, the loss of which would have effects on even global biodiversity! The study provides a gradient score for each ecoregion, from freshwater habitat restoration to conservation (at the least affected end). This will allow the global community to prioritize both management and research efforts for more efficient prevention of the current freshwater biodiversity loss.
The Freshwater Blog 