Blog

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

Velvet spiders include some of the most beautiful arachnids in Europe and some of the world’s most cooperative species. Social species can be very abundant in parts of tropical Africa and Asia with conspicuous colonies dotting the landscape. Social colonies may consist of hundreds of closely-related individuals that participate in dramatic mass attacks on prey (Figure 1) and care for their young. The ecology of these social species is fascinating and has been the subject of several landmark scientific papers. The study was published in a special issue of the open access journal ZooKeys.

By contrast, most kinds of velvet spider are rarely encountered. Most species keep well hidden or dig burrows and live underground. Because of the cryptic habits of most velvet spiders, scientific knowledge of this spider family is uneven to say the least. The name velvet spider accurately describes the dark and shiny appearance of these spiders. Some species also have brightly colored highlights, such as the red, white, and black ladybird spiders of Europe and North Asia (Figure 2). With the exception of one species from Brazil, velvet spiders live in Europe, Asia, and Africa.

The international team assembled to advance basic knowledge about velvet spiders included people and institutions from the Netherlands, Denmark, United States, Czechia, Hungary, and Iran. International collaboration in taxonomic research was the goal of the EDIT (European Distributed Institute of Taxonomy) Integrated Research grant, which provided most of the funding for this project. The team assembled a hefty library of images documenting the anatomy of all the major kinds of velvet spider. This included both portrait-like color photographs and electron micrographs showing details of the spigots that these spiders use to make silk. San Francisco-based artist Giovanni Maki contributed beautiful drawings of the male genitalia. The project also used DNA sequence data to reconstruct the evolutionary history of velvet spiders. The DNA data confirmed that one particularly enigmatic species belongs to a new genus (Figure 3).

In recognition of the fact that this velvet spider lives underground, the new genus has been named Loureedia in a whimsical salute to the musician who began his distinguished career leading the 60s rock band "The Velvet Underground."

In spite of all the progress that this new monograph represents, there is much more work still to be done. Taxonomy is a fundamental science, and advances in it can promote research in other areas. Some of the most obscure groups of velvet spiders from the Mediterranean and Southern Africa will now be more easy to identify and study. This is thanks to the progressive approach taken by publisher Pensoft. The full-color monograph is freely available for download through the web site of the journal ZooKeys. Pictures and descriptions also appear on the wiki web site Species-ID and an interactive map of the specimens used in the study is explorable using Google Earth (please note you must have it installed in order to view the map). So this publically-funded research on a remarkable and often beautiful group of spiders will be freely available not only to scientists but to the public as well.

Original source:
Miller JA, Griswold CE, Scharff N, Řezáč M, Szűts T, Marhabaie M (2012) The velvet spiders: an atlas of the Eresidae (Arachnida, Araneae). ZooKeys 195: 1-144. doi: 10.3897/zookeys.195.2342

Read in Zulu.

Read in Farsi.

Read in Hungarian.

Read in Czech.

Read in Dutch [link].

The Belgian Biodiversity Platform has just released a new website "IFBL Data Portal, Explore Flora Checklists of Belgium". It aggregates about 23,000 checklists of vascular plants in Belgium, compiled since 1939. Users can search a database of over 2.5 million observations of over 2,800 different species. The website will be updated on a monthly basis, in cooperation with the Florabank database.

This website is a result of the cooperation between the Belgian Biodiversity Platform, Flo.Wer, the National Botanic Garden of Belgium and the Research Institute for Nature and Forest (INBO). The data originates from two digitization projects funded by the Belgian Biodiversity Platform (IFBL1 and IFBL2), aiming to digitize data used for the production of the "Atlas of the Belgian and Luxembourg flora", and from Florabank1, the database that deals with the distribution data of the wild flora (indigenous species, archeophytes and naturalised aliens) of Flanders and the Brussels Capital Region.

The website is also helpful for analysis, comparing floral data over successive periods and could be used for the production of Belgian flora atlases.

The database "Florabank1" has been described in a data paper, published in the open access journal PhytoKeys in a collaboration with GBIF. A ‘data paper’ allows data creators to be credited for their work, and also communicates to other scientists that such a dataset has been released and is available freely for re-use in future studies. Such a paper invites others to use the data for any number of purposes immediately, and to provide feedback on any inconsistencies they find. Pensoft Publishers have detailed their "Data Publishing Policies and Guidelines for Biodiversity Data", with the goal to introduce this concept to authors and to help them to start using it effectively.

The data paper combines the static, unchangeable character of a published scientific paper with the dynamic nature of a continuously updated database.

For more information on the IFBL methodology, see here. Institutions dealing with data on vascular plants in Belgium can contact Nicolas Noé to import their data into the IFBL Data Portal: n.noe@biodiversity.be

Original source:
Van Landuyt W, Vanhecke L, Brosens D (2012) Florabank1: a grid-based database on vascular plant distribution in the northern part of Belgium (Flanders and the Brussels Capital region). PhytoKeys 12: 59-67. doi: 10.3897/phytokeys.12.2849

Contacts:
For technical questions, please contact: Nicolas Noe; n.noe@biodiversity.be
For science-related questions, please contact: Wouter Van Landuyt; Wouter.vanlanduyt@inbo.be

Besides the obvious differences between plants and animals, subtle ones lie concealed within the cell, even within the nucleus. In both plant and animal cells, the nucleus contains DNA, which condenses into chromosomes during cell division. Chromosomes can be counted at that stage, revealing the chromosome number for each species. Here comes a difference: while the chromosome number spans a relatively short range across animal species (2-296: 46 in man), some plant species have over 1000 chromosomes. The adder’s-tongue Ophioglossum reticulatum, a fern ally from the tropics, has 1440 chromosomes in its vegetative cells.

High chromosome numbers are generally linked to polyploidy, i.e. the occurrence of more than two haploid sets of chromosomes. In this research, the chromosome number variation of endemic Italian plants was evaluated. Endemics are species that are unique to a defined geographic location, where they establish through some form of isolation – geographic or reproductive – from other species. As polyploidy can bring about reproductive isolation, it was interesting to study to what extent this process was involved in the evolutionary pathway leading to the endemic species of the Italian flora.

Using data from the online database "Chrobase.it", the researchers found that for about 55% of endemic species, the chromosome number is known. Statistical analyses of these chromosome numbers suggest that similar evolutionary trends acted upon endemics and species with wider distribution. Based on estimates for a subset of data, it was also shown that the vast majority (above 70%) of Italian endemics are diploid. The study was published in the open access journal Comparative Cytogenetics.

An intriguing result was obtained by comparing the number of species with even ploidy level (diploid, tetraploid, hexaploid, octoploid, etc.): it was discovered that those parameters are linked by an exponential function, implying that the higher the (even) ploidy level, the lower its frequency in terms of number of species.

The biological implications of this find are not yet clear and must be further investigated. To say the least, this phenomenon opens a new line of investigation in cytogenetics, aimed to clarify the evolutionary mechanisms giving rise to these constant relationships among increasing even ploidy levels.

Original source:
Bedini G, Garbari F, Peruzzi L (2012) Chromosome number variation of the Italian endemic vascular flora. State-of-the-art, gaps in knowledge and evidence for an exponential relationship among even ploidy levels. Comparative Cytogenetics 6(2): 192. doi: 10.3897/CompCytogen.v6i2.3107

A new bright yellow frog species has been found in the mountains of western Panama. The frog belongs to a species-rich group of frogs, the so called rainfrogs that lack a tadpole stage, but develop directly as little frogs inside the egg.

The frog, that measures less than 2 cm, was discovered by Andreas Hertz and his colleagues, who are reptile and amphibian specialists at the Senckenberg Research Institute in Frankfurt am Main; Germany. They discovered it in 2010 during several field trips to the Serranía de Tabasará of western Panama a highly understudied part of the Panamanian central mountain range.

"Although we recognized that the male mating call of this species differs from all what we had heard before and therefore suspected it to be new, much effort was involved to finally spot it in the dense vegetation", said Hertz. "When we finally caught the first individuals by hand, we noticed that it dyes one’s fingers yellow when it is handled. The scientific name (Diasporus citrinobapheus) of this new frog refers to this characteristic and means yellow dyer rainfrog."

To assure the validity of the frog as a new species, the biologists studied body structure, coloration, molecular genetic data, and vocalizations of a series of individuals, and compared the results with the data derived from closely related species.

Additionally, the researchers took into consideration the possibility that the yellow stain may be poisonous and performed an analysis of skin secretions. "We cannot say whether the dye is any good as a predatory defence, as we could not find any poisonous components. Maybe the colour is just easily washed out and has no particular function. However, for now, this peculiarity of the new species remains enigmatic." said Hertz.

Original source:
Hertz A, Hauenschild F, Lotzkat S, Köhler G (2012) A new golden frog species of the genus Diasporus (Amphibia, Eleutherodactylidae) from the Cordillera Central, western Panama. ZooKeys 196: 23-46. doi: 10.3897/zookeys.196.2774

Additional Information:
Research in Panama by the Herpetological Section at the Senckenberg Research Institute
Köhler G (2011) Amphibians of Central America. Herpeton Verlag Elke Köhler, Offenbach, Germany, 378 pp.

Northwestern Europe harbors one of the best known biotas, thanks to the long faunistic and floristic traditions practiced there. However, some animal groups are far better known than others. The diversity of true flies there is fascinating, and undescribed species of flies, midges and gnats are not uncommon. Because Northwestern Europe was almost totally glaciated as recently as 10 000 years ago, endemic animal species of that region are generally lacking, or are exceptions. Hence, most NW European insects and other species have colonized the area following the withdrawal of ice.

The new crane fly species Tipula recondita, is not an exception. It was found on both extremes of the vast Eurasian continent, in Northern Finland (Kittilä) as well as in the Russian Far East (Primorski kray). The description was published in the open access journal ZooKeys.

PhD candidate Jukka Salmela, working in the Zoological Museum in Turku (Finland), thinks that the new species is most likely a very rare one, because the Finnish fauna has been intensively studied during the 2000s. The rarity of the species is perhaps caused by its association with the increasinlgy rare old-growth forests and / or calcareous herb-rich forests of the taiga. Both old-growth forests with large amounts of decaying trees and northern herb-rich forests are rare habitats in Northwestern Europe.

In addition to morphology, DNA barcoding was used to assess the status of the new species. Intraspecific genetic distance between Finnish and Russian populations was small, verifying the idea of a single but disjunct species; geographic distance of the populations is over 6500 km. Moreover, based on morphology and DNA, the new species is clearly separated from closely related species. "The sequencing result was expected, because among crane flies, there are some other wide-ranging and disjunct species, e.g. Tipula kaisilai and T. subexcisa. These disjunct populations may be relicts from climatically more favourable periods, when these species were more widespread. On the other hand, it can’t be excluded that some disjunct species are more common than we currently know; the efforts directed at collecting them may simply have been too low to reveal their true ranges. However, both DNA and morphology suggest that the Finnish and Russian populations belong to the same species", said Salmela. "The next step is to map the occurrence of the species in NW Europe and arrive at a better understanding of its ecology; a larva or two would be nice to catch", Salmela added.

Original source:
Pilipenko VE, Salmela J, Vesterinen EJ (2012) Description and DNA barcoding of Tipula (Pterelachisus) recondita sp. n. from the Palaearctic region (Diptera, Tipulidae). ZooKeys 192: 51-65. doi: 10.3897/zookeys.192.2364

Researchers at Auburn University have reported the discovery a new trapdoor spider species from a well-developed housing subdivision in the heart of the city of Auburn, Alabama. Myrmekiaphila tigris, affectionately referred to as the Auburn Tiger Trapdoor spider, is named in honor of Auburn University‘s costumed Tiger mascot, Aubie.

The research team, directed by Biological Sciences professor Jason Bond, lead investigator and director of the Auburn University Museum of Natural History, and Charles Ray, a research fellow in the Department of Entomology & Plant Pathology, was excited at the prospect of such a remarkable find just underfoot. Bond and Ray actually live in the neighborhood where the new species was discovered. The study was published in the open access journal ZooKeys and is freely available under a Creative Commons Attribution license.

Myrmekiaphila tigris belongs to a genus that contains 11 other species of trapdoor spider found throughout the eastern U.S. and includes the now-famous species Myrmekiaphila neilyoungi, from Birmingham, Alabama, named for Canadian rocker Neil Young.

Trapdoor spiders – related to tarantulas, funnel web spiders, and their kin – construct subterranean burrows that they cover with a hinged door made of a mixture of silk and soil. Female spiders spend nearly their entire lives in a single silk-lined burrow from which they forage as sit-and-wait predators. Prey are captured, usually at night, when an insect or other animal causes a vibration, provoking the spider to leap from the burrow entrance, bite and envenomate the unsuspecting victim, and then return to the bottom of the burrow to feast on its prize.

Due to superficial similarities, Myrmekiaphila tigris was previously believed to be a different species, M. foliata, according to a taxonomic study of the group that was published a few years ago. However, closer examination revealed considerable differences in appearance, particularly in their genitalia, that were supported by additional studies comparing the DNA of M. tigris with that of related species: "Despite the physical uniqueness of these specimens, the use of DNA as an alternate, less subjective line of evidence for recognizing the species was warranted, given our excitement with discovering a new species literally in our own backyards," Bond said.

Members of the species are rarely encountered individually. However, once males reach sexual maturity at around 5 or 6 years old, they emerge from their burrows to find a female with which to mate; shortly thereafter they die. Wandering males can be found in relatively large numbers on neighborhood sidewalks, in swimming pools and even in homeowners’ garages for a brief time during the months of November and December. Females, on the other hand, are much more secretive, living relatively long, 15 to 20-year lives in their below-ground burrows. They often have more intricate burrows that include side chambers with additional underground trapdoors. Burrows can be found along the banks in relatively young, secondary growth forests in neighborhood natural areas.

Bond said, "The discovery of a new species in a well-developed area like this further demonstrates the amount of biodiversity on our planet that remains unknown; we know so little about our home planet and the other organisms that inhabit it with us." According to some estimates, scientists have managed over the course of the past 250 years to describe only a few million of the 10 to 30 million of Earth’s species.

Original source:
Bond JE, Hamilton CA, Garrison NL, Ray CH (2012) Phylogenetic reconsideration of Myrmekiaphila systematics with a description of the new trapdoor spider species Myrmekiaphila tigris (Araneae, Mygalomorphae, Cyrtaucheniidae, Euctenizinae) from Auburn, Alabama. ZooKeys 190: 95-109. doi: 10.3897/zookeys.190.3011

Additional information:
In: Bond JE and N.I. Platnick. 2007. Taxonomic review of the trapdoor spider genus Myrmekiaphila (Araneae: Mygalomorphae: Cyrtaucheniidae). American Museum Novitates, 3596: 1-30.

Pensoft Publishers are pleased to inform you that a PhytoKeys paper, by Natalia Filipowicz, Michael Nee and the journal’s editor, Susanne Renner, was featured in a Scientific American article: Genome Run: Andean Shrub Is First New Plant Species Described by Its DNA.

Original source:
Filipowicz N, Nee MH, Renner SS (2012) Description and molecular diagnosis of a new species of Brunfelsia (Solanaceae) from the Bolivian and Argentinean Andes. PhytoKeys 10: 83–94. doi: 10.3897/phytokeys.10.2558

Related press release on EurekAlert.