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Session 1: Discovery: It’s all about the metadata? Or is it?

Vishwas Chavan, GBIF

Towards next generation (data inclusive) publishing

The Open Access Infrastructure for Research in Europe, or OpenAIRE, has conducted an interview with the Managing Director and Founder of Pensoft Publishers, Prof. Lyubomir Penev. The interview soncerns the new type of scholarly paper, designed in collaboration between Pensoft Publishers and the Global Biodiversity Information Facility (GBIF), and rapidly gaining popularity: the Data Paper.

Read the full text of the interview here.

In a special issue of ZooKeys, initiated by the Natural History Museum London, Vince Smith and Vladimir Blagoderov bring together 18 papers by 81 authors to look at progress and prospects for mass digitising entire natural history collections.

Centuries of exploration and discovery have documented the diversity of life on Earth. Records of this biodiversity are, for the most part, distributed across varied and distinct natural history collections worldwide. That has made the task of assessing the information in these collections an immense challenge, the largest of which is how to capture specimen data fast enough to achieve digitisation of entire collections while maintaining sufficient data quality.

Now, an effort is underway to digitise major collections to unlock their research potential and provide unlimited access to the public. This series of eighteen articles in the open-access journal ZooKeys examines recent advances in imaging systems and data gathering techniques, combined with more collaborative approaches to digitisation. These provide a snapshot of progress toward the creation of a global virtual natural history museum.

“As a sample of the natural world, these collections underpin our understanding of ecosystems, biodiversity and the sustainable use of natural resources” says Vince Smith, Cybertaxonomist at the Natural History Museum London. “Technical innovations in digitising hardware, software and data interactions are now making it possible to conceive of wholly digital collections, creating a new frontier for natural history research”.

Examples of research covered by these articles include a description to efforts digitise 30 million plant, insect and vertebrate specimens at NCB Naturalis in the Netherlands; new scanning and telemicroscopy solutions to digitise the millions of pinned insect specimens held in the Australian National Insect Collection and its European and North American counterparts; citizen science projects being used to crowdsource the transcription of thousands of specimen labels and field notebooks; and new data portals providing central access to millions of biological specimens across Europe.

Original source:
Blagoderov V, Smith VS (2012) Bringing collections out of the dark. In: Blagoderov V, Smith VS (Ed) No specimen left behind: mass digitization of natural history collections. ZooKeys 209: 1-6. doi: 10.3897/zookeys.209.3699

Additional Information:
InvertNet http://invertnet.dyndns.org/
Notes from Nature http://www.notesfromnature.org/
Heteroptera Species Pages http://research.amnh.org/pbi/heteropteraspeciespage/
Field Notes of Junius Henderson http://en.wikisource.org/wiki/Field_Notes_of_Junius_Henderson
OpenUp!  http://open-up.eu/
Morphbank-ALA http://morphbank.ala.org.au/
DScan in action http://youtu.be/zyT7l-CZego
North Carolina State University Insect Museum http://insectmuseum.org/
NCSUIM collection: http://www.gigapan.com/users/ncsuinsectmuseum/gigapans

Plant overcomes infertility to give rise to a new species in Scotland

A new species of monkey flower, created by the union of two foreign plant species, has been discovered on the bank of a stream in Scotland. Genetic changes in this attractive yellow-flowered hybrid have allowed it to overcome infertility and made it a rare example of a brand new species that has originated in the wild in the last 150 years. Thousands of wild species and some crops are thought to have originated in this way, yet only a handful of examples exist where this type of species formation has occurred in recent history.

The ancestors of the new plant were brought from the Americas as botanical curiosities in the 1800s and were quickly adopted by Victorian gardeners. Soon after their arrival, they escaped the confines of British gardens and can now be found growing in the wild, along the banks of rivers and streams. Reproduction between these species produces hybrids that are now widespread in Britain. Yet, genetic differences between the two parents mean that the hybrids are infertile and cannot go beyond the first generation.

Dr Mario Vallejo-Marin, a plant evolutionary biologist at the University of Stirling, has documented the first examples of hybrid monkey flowers that have overcome these genetic barriers and show fully restored fertility. This fertile hybrid derived from ‘immigrant’ parents represents a new species, native to Scotland. Dr Vallejo-Marin has chosen to name this species Mimulus peregrinus, which translates as ‘the wanderer’. The species is described in the open access journal PhytoKeys.

‘The two American monkey flowers are unable to produce fertile hybrids due to differences in the amount of DNA present in each species, the equivalent of getting a sterile mule from crossing a horse and a donkey’, said Dr. Vallejo-Marin. ‘However, in rare cases, duplication of the entire hybrid DNA, known as polyploidization, can balance the amount of DNA and restore fertility. Our studies suggest that this is what has happened here.’

The discovery will help scientists to understand how new species form. It is thought that many existing plant species including crops such as wheat, cotton and tobacco may have originated in a similar way, but finding examples of this process in action is rare. ‘This is an exciting opportunity to study evolution as it happens,’ said Vallejo Marin. ‘We do not yet know how common the new species is or how well it will fare, so the next step will be to find out its distribution and whether its ecological characteristics, allow it to colonise environments that cannot be currently exploited by its parents.’

Original source:
Vallejo-Marín M (2012) Mimulus peregrinus (Phrymaceae): A new British allopolyploid species. PhytoKeys 14: 1-14. doi: 10.3897/phytokeys.14.3305

The northern part of the North Island of New Zealand is marked at approximately 38° S latitude by a distinct ecological boundary known as the "kauri line". This region forms the southern distributional limit of many plants and is the warmest part of New Zealand. A number of endemic plants are found there. Ecologists have recently discovered a new species of wirerush from peatlands north of the "kauri line".

Wetlands serve vital ecological functions by providing wildlife habitat, carbon storage, nutrient regulation and water balance. New Zealand has a number of wetland types. The peat-forming wetlands are dominated by a plant commonly known as wirerush (Empodisma, Restionaceae). The name Empodisma is derived from a Greek word meaning "to hinder". Both the common and the Greek name describe its dense scrambling growth form. Empodisma is in the southern hemisphere family Restionaceae.

The horizontal root systems of wirerush branch profusely forming finely divided rootlets with long-lived root hairs. In wirerush bogs, the underlying peat is formed largely from the remains of the root systems, stems bases and trapped plant litter. The peat mass absorbs water like a sponge. In peat bogs, incoming rainfall and atmospheric particles are the only source of nutrients. These are removed from the flow of water in the porous upper layers of peat. This may be an adaptive feature in nutrient-poor environments such as peat bogs.

Steve Wagstaff and Beverly Clarkson recognize three species of wirerush including the newly described species Empodisma robustum. Empodisma robustum is only found in peatlands in northern New Zealand, whereas E. minus is found in central and southern New Zealand and eastern Australia, and E. gracillimum is restricted to western Australia. Their study provides an account of the origin, diversification and ecology of the genus with descriptive keys and illustrations.

Original source:
Wagstaff SJ, Clarkson BR (2012) Systematics and ecology of the Australasian genus Empodisma (Restionaceae) and description of a new species from peatlands in northern New Zealand. PhytoKeys 13: 39-79. doi: 10.3897/phytokeys.13.3259

Data Papers are a new type of scholarly articles, which are rapidly gaining momentum in the scientific community. They are peer-reviewed scholarly publications that describe data sets and provide an opportunity for data authors to receive the academic credit through citation and re-use of the published data. Data Papers of this kind have been recently published in cooperation among the international organization Global Biodiversity Information Facilities (GBIF) and the journals ZooKeys and PhytoKeys.

Most online keys to identify biodiversity (e.g., species and genera) are usually based on structured data. There are several software packages to create interactive keys; however a significant deficiency of them is the lack of a permanent scientific record and of a proper citation mechanism. Now, a new initiative is being put forward, for establishing the Online Identification Key (OIK) as a new type of scientific article, that is a derivative of the Data Paper. The model is illustrated by an exemplar paper describing a new software platform for creating online keys, MOSCHweb. The paper and an associated editorial piece are published in the open access journal ZooKeys.

"MOSCHweb is a new software platform that facilitates constructing of online identification keys. Our ZooKeys paper describes the main features of an interactive key to the Euro-Asiatic genera of tachinid flies implemented as an original web application and discusses briefly the advantages of these tools for both biologists and general users", said the lead author Dr Pierfilippo Cerretti from the University of Roma ‘La Sapienza’.

"The publication of an online key in the form of a scholarly article is a pragmatic compromise between the dynamic structure of the internet and the static character of scientific articles. The authors of the key will be able to continuously update their product, to the benefit of its users. At the same time, the users will have available a citation mechanism for the online key, identical to that used for any other scientific article, to properly credit its authors" commented Prof. Lyubomir Penev, founder and managing director of Pensoft Publishers.

The elaboration of the data paper format was funded in part by the European Union’s FP7 project ViBRANT.

Original sources:
Penev L, Cerretti P, Tschorsnig H-P, Lopresti M, Di Giovanni F, Georgiev T, Stoev P (2012) Publishing online identification keys in the form of scholarly papers. ZooKeys 205: 1-3. doi: 10.3897/zookeys.205.3581

Cerretti P, Tschorsnig H-P, Lopresti M, Di Giovanni F (2012) MOSCHweb — a matrix-based interactive key to the genera of the Palaearctic Tachinidae (Insecta, Diptera). ZooKeys 205: 5-18. doi: 10.3897/zookeys.205.3409

The Impact Factor of ZooKeys has increased from 0.517 to 0.897. ZooKeys’ growth continues: 219 articles and 5334 pages were published in the first half of 2012.

One of the realities of modern science is that publications and citations are key metrics when evaluating performance impact of scientists. Data papers can be compared to papers describing a newly found taxon: the articles have a standard format and data set users will cite the data paper in a manner, similar to how scientists cite authority when mentioning a scientific name. Thus, scientists contributing data sets will also gain publication credit, while the number of citations their data set generates will provide a way of measuring the scientific value of the data.

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.

Read full text here.

On 5th of June 2012, Zookeys published its 200th jubilee issue. The journal continues to experience steady growth ever since its inception in 2008. Since the start of 2012, the journal reported 164% increase of the number of published articles (202), in comparison to the same period of the previous year (123). The number of published issues has also increased, from 29 to 40 for the same timeframe. Additionally, ZooKeys continues to evolve it’s editorial workflow, constantly implementing new and improved publishing and dissemination technologies, always striving to be on point for digital biodiversity science.

The jubilee issue is a monograph, devoted to the ants in the Philippines. The authors encounter more than 90 genera of ants, native to the archipelago, with 3 genera entirely new to science. 12% of the species are recorded for the first time in the region. The Philippines is considered one of the hottest of the biodiversity hotspots, though imposed to a severe human pressure on its highly endemic (unique) native flora and fauna. Despite decades of nature conservation measures and reforestation, natural habitats continue to dwindle. Aside from habitat destruction, invasive ant species also impact the native ones, although the extent and severity of this influence is yet to be determined.

ZooKeys 200

Original source citation:
General DM, Alpert GD (2012) A synoptic review of the ant genera (Hymenoptera, Formicidae) of the Philippines. ZooKeys 200: 1-111. doi: 10.3897/zookeys.200.2447

Biologists Leonard Freed and Rebecca Cann from the University of Hawaii at Manoa have been studying birds at Hakalau Forest National Wildlife Refuge for 20 years. Located on an old cattle ranch on the windward slope of Mauna Kea on the Island of Hawaii, it was established in 1985 to protect 8 species of rare and endangered perching birds. The refuge and its volunteers planted over 400,000 seedlings of native koa trees in an abandoned pasture to restore high elevation forest. The once-rare white-eye colonized the restoration area, grew rapidly in it, but then surged into the old-growth forest below. Freed and Cann estimated that tens of thousands of native birds were lost. Their study was recently published in the open access journal NeoBiota.

The researchers had previously shown competition between white-eyes and native birds on their study sites. With increased numbers of white-eyes, young of all native species measured had stunted growth, indicating that food was becoming a problem. They also documented that birds of all ages had difficulty replacing their feathers. Each problem, both unprecedented in nature, occurred at the same time. In contrast to the forest adjacent to the restoration area, native birds deeper within the forest had normal growth and feather replacement where white-eyes were still rare.

Freed and Cann then used the refuge’s own survey data collected over 3,373 ha of open forest and 1,998 ha of closed forest to determine if changes observed on their study sites were a general problem on the entire refuge. They documented a stepwise increase in density of white-eyes in the open forest area that had been sustained for 8 years between 2000 and 2007, and a more gradual increase in the closed forest area below that.

Loss of native birds followed the refuge-wide surge of white-eyes. Greater declines occurred in the open forest area where white-eyes increased first, amounting to a drop of one-third of native birds. About 10% of birds disappeared from the closed forest area, but there was strong correlation among losses of native species in the two areas. The researchers expect that losses in the more pristine closed forest area will continue, because the white-eye is still increasing there. Ironically, only an alien species is increasing on a refuge set aside to protect native Hawaiian birds. Forest restoration has precipitated a problem that requires additional action in the forest below. Hawaiian birds are considered to be “conservation reliant” species from other threats. Now the future of native birds on the refuge requires control of an introduced bird.

Original source:
Freed LA, Cann RL (2012) Increase of an introduced bird competitor in old-growth forest associated with restoration. NeoBiota 13: 43-60. doi: 10.3897/neobiota.13.2946