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Huge data encompassed into a unique georeferenced macrobenthic assemblages database

A new peer-reviewed data paper offers a comprehensive, open-access collection of georeferenced biological information about the Antarctic macrobenthic communities. The term macrobenthic refers to the visible-for-the-eye organisms that live near or on the sea bottom such as echinoderms, sponges, ascidians, crustaceans. The paper will help in coordinating biodiversity research and conservation activities on species living near the ocean bottom of the Antarctic.

The data paper "Antarctic macrobenthic communities: A compilation of circumpolar information", published in the open access journal Nature Conservation, describes data from approximately 90 different expeditions in the region since 1956 that have now been made openly available under a CC-By license. The paper provides unique georeferenced biological basic information for the planning of future coordinated research activities, for example those under the umbrella of the biology program Antarctic Thresholds – Ecosystem Resilience and Adaptation (AnT-ERA) of the Scientific Committee on Antarctic Research (SCAR). The information collected could be also beneficial for current conservation priorities such as the planning of Marine Protected Areas (MPAs) by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR).

The expeditions were organised by several famous explorers of the Antarctic. The area covered by the paper consists of almost the entire Southern Ocean, including sites covered by a single ice-shelf. The vast majority of information is from shelf areas around the continent at water depth shallower than 800m. The information from the different sources is then attributed to the classified macrobenthic assemblages. The results are made publicly available via the "Antarctic Biodiversity Facility" (data.biodiversity.aq).

A specific feature of this paper is that the manuscript was automatically generated from the Integrated Publishing Toolkit of the Antarctic Node of the Global Biodiversity Information Facility (AntaBIF IPT) and then submitted to the journal Nature Conservation through a novel workflow developed by GBIF and Pensoft Publishers. (see previous press release). Data are made freely available through the AntaBIF IPT, and sea-bed images of 214 localities through the data repository for geoscience and environmental data, PANGAEA- Data Publisher for Earth and Environmental Science (sample: http://doi.pangaea.de/10.1594/PANGAEA.198682).

Speaking from on board the research vessel ‘Polarstern’, the paper’s lead author Prof. Julian Gutt of the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Germany commented:

"The most important achievement of this paper is that data collected over many years and by various institutions are now not only freely available for anyone to download and use, but also properly described to facilitate future work in re-using the data. The Data Paper concept is certainly a great approach that multiplies the effect of funds and efforts spent by generations of scientists."

The data will also be used for a comprehensive Biogeography Atlas of the Southern Ocean project to be released during the XI SCAR Biology Symposium in Barcelona July 2013.

 

 

Published by Pensoft Publishers.

ORIGINAL SOURCE:

Gutt J, David B, Lockhart SJ, van de Putte A (2013) Antarctic macrobenthic communities: A compilation of circumpolar information. Nature Conservation 4: 1–12. doi: 10.3897/natureconservation.4.4499

Contacts:

Dr. Julian Gutt
Alfred Wegener Institute
Helmholtz Centre for Polar and Marine Research
Email: julian.gutt@awi.de

Dr Vishwas Chavan
Global Biodiversity Information Facility (GBIF)
Copenhagen, DENMARK
Tel. 45-35-32-14-75, Fax. 45-35-32-14-80
Email: vchavan@gbif.org

Additional Information:

What is a Data Paper?

A Data Paper is a scholarly journal publication whose primary purpose is to describe a dataset or a group of datasets, rather than to report a research investigation. As such, it contains facts about data, not hypotheses and arguments in support of those hypotheses based upon data, as found in a conventional research article. Its purposes are three-fold:

to provide a citable journal publication that brings scholarly credit to data publishers;
to describe the data in a structured human-readable form;
to bring the existence of the data to the attention of the scholarly community.

Sources:

Chavan V, Penev L (2011) The data paper: a mechanism to incentivize data publishing in biodiversity science. BMC Bioinformatics, 12 (Suppl 15): S2. doi: 10.1186/1471-2105-12-S15-S2

Penev L, Mietchen D, Chavan V, Hagedorn G, Remsen D, Smith V, Shotton D (2011). Pensoft Data Publishing Policies and Guidelines for Biodiversity Data.
http://www.pensoft.net/J_FILES/Pensoft_Data_Publishing_Policies_and_Guidelines.pdf

A new species of scorpion, Vaejovis brysoni, was found in the Santa Catalina Mountains in southern Arizona. Another scorpion of the same group also inhabits this mountain range, making this the first documented case of two vorhiesi group species distributed on the same mountain. The study was published in the open access, peer-reviewed journal Zookeys.

These mountains overlook the city of Tucson, Arizona. Amazingly, in the 21st century, there are still new species to be discovered right here in the United States. What is even more surprising is that the new species was found within sight of a large metropolitan area.

Recently Dr. Rob Bryson Jr. discovered this new species while looking for a completely different animal. Many important discoveries are made this way by scientists who start out working on something completely different. He sent specimens to the authors, who determined that they were indeed a new scorpion species. At that point, the team was assembled and the rest is history.

For over 50 years only four species of mountain scorpions were known from the state of Arizona. That number has more than doubled over the past six years, with a total of 10 species now known, all belonging to the same group. Arizona is known for isolated mountain habitats in the desert known as Sky Islands. These Sky Islands are where the new species are being discovered.
"This latest new scorpion is a prime example of the amazing diversity of life still to be discovered, right here in 21st century America.", adds Richard F. Ayrey, one of the co-author of the original article.

 Original Source:

Ayrey RF, Webber MM (2013) A new Vaejovis C.L. Koch, 1836, the second known vorhiesi group species from the Santa Catalina Mountains of Arizona (Scorpiones, Vaejovidae). ZooKeys 270: 21–35, doi: 10.3897/zookeys.270.4500.

 

Forcepflies are usually known as earwigflies, because the males have a large genital forceps that resembles the cerci of earwigs. A new species of forcepfly Meropeidae (Mecoptera) from Brazil was described, representing only the 3rd extant species described in this family and the 1st record of the family from the Neotropical region. The distribution and biogeography of the family are discussed and it is even proposed that Meropeidae originated before continental drift and then divided into two branches, northern and southern, with the breakup of the old supercontinent Pangea. The study was published in the open access journal ZooKeys.

Despite all previous collecting efforts in this area the species had never been recorded before. The specimen was collected in a private ranch near a forest fragment surrounded by farms in the Atlantic Forest biome, one of the most threatened in Brazil. It can be found in a variety of habitats, including woodland, Jarrah forest, and sand plain vegetation. What makes forcepflies special is the fact that little is known about their biology and the immature stages remain a mystery to scientists. The adults, who are nocturnal and seem to live on the ground, are also capable of stridulation, or the production of sound by rubbing certain body parts.

"The discovery of this new relict species is an important signal to reinforce the conservation of Brazilian Atlantic Forest biome. Certainly there are many more mecopterans species yet to be discovered in these forests", said the lead author Dr Renato Machado from the Texas A & M University, College Station, USA.

 

 

Original Source

Renato Jose Pires Machado, Ricardo Kawada, José Albertino Rafael (2013) New continental record and new species of Austromerope (Mecoptera, Meropeidae) from Brazil. ZooKeys 269: 1–10. doi: 10.3897/zookeys.269.4240.

 

The article “The amphibians and reptiles of Luzon Island, Philippines, VIII: the herpetofauna of Cagayan and Isabela Provinces, northern Sierra Madre Mountain Range”, recently published in the open access, peer reviewed journal Zookeys, has gained incredible popularity through uploading all images to Wikimedia Commons.

Thanks to the rich, high resolution illustrations featured in the article, all figures have been since ported to Wikimedia Commons (the media repository used by Wikipedias, Wikispecies and their sister projects), and till date, they have been used on well over 300 pages across some 30 languages.

The same Images are also automatically exported by the journal on the day of its publication to Encyclopedia of Life and the Wiki species descriptions catalogue Species-ID.

All authors are encouraged to submit high resolution quality figures and videos to be featured in their articles and achieve the same level of dissemination.

Reference:

Brown RM, Siler CD, Oliveros CH, Welton LJ, Rock A, Swab J, Van Weerd M, van Beijnen J, Jose E, Rodriguez D, Jose E, Diesmos AC (2013) The amphibians and reptiles of Luzon Island, Philippines, VIII: the herpetofauna of Cagayan and Isabela Provinces, northern Sierra Madre Mountain Range. ZooKeys 266: 1-120. doi: 10.3897/zookeys.266.3982

The newly described species might benefit the development of organic rice farming

The semi-aquatic earthworms in the genus Glyphidrilus are somewhat unfamiliar species that live between the terrestrial and freshwater ecosystems of rivers, streams, canals, ponds, swamps and paddy systems. Remarkably, each species is endemic to a single water basin, carrying its own signature of evolution from their common origin. A study describing ten newly discovered species of the genus has been published in the open access journal ZooKeys.

In Thailand, the species demonstrate astonishing biodiversity due to the monsoon climate contributing to drastic river system changes and a large variety of microhabitats. While general interconnections among these allow for gene flow, their great diversity leads to independent evolution and specialization in isolation.

The animals orient themselves vertically, with their bodies in the wet soil along the banks and tails placed on the soil surface. Among the interesting characteristics of these worms is a rounded body tip, while the end is square shaped. When twisted, the posterior end, which is normally above the soil surface, forms U-shaped channels. These are used to allow water circulation down the burrow. This is probably an evolutionary adjustments that ensures oxygen transport to the deeper surface of the worms, while their bodies remain in the burrows.

Another peculiar feature are the so-called "wings", or the expanded part of epidermis near the body tip. The function of the wings is still unknown to scientists, but it has been suggested that they evolved to assist breathing in such aquatic habitats. Because the wings will be located deep in the burrow at a low oxygen supply and are absent in sexually immature juveniles, a more conventional explanation might be that they are used to aid copulation rather than respiration.

Among the natural habitats of these worms are the rice fields in Thailand, which serve as a reservoir and breeding ground for the animals. The worms turn out to play an important role in the development of rice farming, being a facilitator in the decomposition of organic matter to be a natural fertilizer, as well as improving the soil properties for better rice root system. The species also assist the release of essential minerals in some chemical fertilizers, though not in pesticides, which prove to be lethal to the worms.

The increased use of pesticides in agriculture puts these species in danger. The author Dr. Somsak Panha, from the Animal Systematics Research Unit, Chulalongkorn University in Bangkok, Thailand, comments: "The worms will survive in areas using chemical fertilizers but not those using chemical pesticides. However, the worms did well in areas of organic farming and so are likely to be sensitive to modern agrochemical contamination of the environment. They may play an important role in organic rice farming."

Original Source:

Chanabun R, Sutcharit C, Tongkerd P, Panha S (2013) The semi-aquatic freshwater earthworms of the genus Glyphidrilus Horst, 1889 from Thailand (Oligochaeta, Almidae) with re-descriptions of several species. ZooKeys 265: 1. doi: 10.3897/zookeys.265.3911

In response to several inquiries, we have now published the following FAQs to facilitate society journals that want to move to advanced open access publishing: http://www.pensoft.net/FAQ-by-society-journals.

 A recent study of the amphibians and reptiles of Sierra Madre Mountain Range, northeastern Luzon, reveals a preliminary enumeration of more than 100 species that contribute to the unique biodiversity of the region. At present, the Luzon region’s herpetological range stands at more than 150 species. Out of these, a total of 49 amphibian species have been documented, 44 of which are native and a remarkable 32 endemic. In the world of reptiles, Luzon can boast with 106 native species, 76 of which are unique to this region.

The catalogue published in the open access journal Zookeys features a fascinating range of reptiles and amphibians, such as the beautifully coloured colubrid snake Hologerrhum philippinum, which is one of the four endemic snake genera from the region and can be recognized by the vibrant-yellow skin decoration. Another species that provokes amazement is the bizarre soft-shell turtle Pelochelys cantorii. The variety described in this study includes fascinating frogs, crocodiles, snakes, lizards and many more, offering a menagerie of shapes and colours all documented in stunning photography.

With such a great array of biodiversity, the northern Philippines has been the focus of of large numbers of new species discoveries and re-discoveries of new species in recent decades, establishing it as a major regional biodiversity hotspot. The herpetological diversity of the island may grow to as many as 90-100 (70-80% endemic) amphibian species and as many as 150-160 reptiles with the contributions of ongoing biodiversity studies in the near future. It will be a major challenge to monitor these communities through time in order to assess their responses to land use changes, climate change, resource extraction, introduced species, emerging infectious disease, and habitat degradation.

With the initial baseline information provided in the survey, tremendous opportunities exist for future studies in taxonomy, biogeography, ecology and conservation of northern Luzon’s amphibians and reptiles. Conservation of Luzon’s vertebrate biodiversity remains an on-going effort, challenged by rapid development,logging, mining and conversion of natural habitats into agricultural lands to provide food for a burgeoning human population.

 

 

Original Source 
Brown RM, Siler CD, Oliveros CH, Welton LJ, Rock A, Swab J, Van Weerd M, van Beijnen J, Jose E, Rodriguez D, Jose E, Diesmos AC (2013) The amphibians and reptiles of Luzon Island, Philippines, VIII: the herpetofauna of Cagayan and Isabela Provinces, northern Sierra Madre Mountain Range. ZooKeys 266: 1-120. doi: 10.3897/zookeys.266.3982

27 new moth species described in the latest issue

Since its inception in 2009, the "Contributions to the systematics of New World macro- moths" series in ZooKeys has been playing an important role in publishing taxonomic changes and new discoveries concerning moth diversity in North America. With a total of 49 publications by 38 authors, this well-established series is among the topic leaders, alongside publications such as Canadian Staphylinidae.

Geographic coverage in Zookeys has previously focused primarily on the North American fauna (Canada, United States and Mexico). This issue marks a rapid acceleration in contributions concerning tropical areas: its articles expand the geographic reach to regions from all over North and South America, the adjacent islands and territories.

The total of 27 new species described in this issue includes moths from North America, Venezuela, Brazil, Argentina and the Dominican Republic. Among the more interesting ones are 5 newly described additions to the particularly big family of Neotropical tigermoths. As the name suggests, they can be easily recognized by their wing decoration that imitates the fur pattern of a big cat.

Another newly described species that could be of great interest was found near the Brazilian Airport, Salvador. Despite its modest looks, this animal could potentially be used for biological control in Florida against the invasive and problematic Brazilian peppertree, which is the natural habitat and food for these moths.

Original Source:

Schmidt BC, Lafontaine JD (2013) Contributions to the systematics of New World macro-moths IV. In: Schmidt BC, Lafontaine JD (Eds) Contributions to the systematics of New World macro-moths IV. ZooKeys 264: 1. doi: 10.3897/zookeys.264.4687

Dr Michael Pogue, a Research Entomologist in the ARS Systematic Entomology Laboratory, at the Smithsonian Institution, Washington, DC, was sent a series of moth specimens from Bahia, Brazil, for identification. The insects were under consideration as a possible biocontrol agent for the invasive Brazilian peppertree in Florida.

‘The species was initially identified as a common species, but when comparisons were made, it became evident that there were multiple species involved’ said Dr. Pogue. Using characters from the moths’ male and female genitalia, Dr. Pogue determined that the so-called ‘common’ species actually consisted of six new species, plus two described species.

Brazilian peppertree is one of the most damaging invasive species in Florida. Originally introduced as an ornamental plant into Florida at least three times in the mid- to late 1800’s, it has since invaded a number of habitats throughout southern and central Florida. In addition to this new biocontrol species, two other species (one new) native to Florida also feed on Brazilian peppertree. The potential biocontrol species had been described previously, but the remaining five new species were described in the present study in ZooKeys.

‘What was interesting about this identification was the discovery of so many new species’, said Dr Pogue. ‘The wing pattern was similar among these species, but their reproductive systems were quite different’. ‘It became obvious that multiple cryptic species were involved only when these dissections were made.’

Cryptic species complexes can be confusing and require proper careful assessment of morphological or molecular characters in order to allow for identifications.

 

 

Original Source:

Pogue MG (2013) A review of the Paectes arcigera species complex (Guenée) (Lepidoptera, Euteliidae). In: Schmidt BC, Lafontaine JD (Eds) Contributions to the systematics of New World macro-moths IV. ZooKeys 264: 125–163. doi: 10.3897/zookeys.264.3274

Taxonomy – the discipline that defines and names groups of organisms – is a field of science that still employs many of the methods used during the beginnings of the discipline in the 18th century. Despite the increasing use of molecular information to delineate new species, the study of the morphology of specimens remains one of the major tasks of taxonomists. These studies often require first-hand examination of the reference specimens (so-called type material) deposited at museum collections around the globe – a time-consuming and laborious task.

To facilitate this procedure, a group of researchers from the Hellenic Centre for Marine Research (HCMR) are exploring the possibilities offered by 3D digital imaging. In a recent article published in the open-access journal ZooKeys, the researchers use X-ray computed tomography to create digital, three-dimensional representations of tiny animals, displaying both internal and external characteristics of the specimens at a detail level similar to that of the microscope.

To demonstrate their method, the researchers imaged a number of polychaete species (marine bristle-worms)—the choice of this group being obvious to Sarah Faulwetter, the leading author, because "despite being ecologically very important, these animals exhibit a fascinating diversity of forms and tissue types, allowing to test the methodology across a range of samples with different characteristics".

The resulting interactive 3D models allow any researcher to virtually rotate, magnify or even dissect the specimen and thus extracting new scientific information, whereas the structure and genetic material of the analysed specimen are kept intact for future studies.
The team stress the importance of 3D imaging methods for taxonomy on its way into the twenty-first century: "Our vision for the future is to provide a digital representation of each museum specimen, simultaneously accessible via the internet by researchers and nature enthusiasts worldwide," says the team leader, Dr Christos Arvanitidis from HCMR.

The instant accessibility of specimens will speed up the creation and dissemination of knowledge. As the authors point out, "human efforts, combined with novel technologies, will help taxonomy to turn into a cyberscience whose discoveries might rival those made during the great naturalist era of the nineteenth century."

See also the playlist in the Pensoft video channel at http://www.youtube.com/playlist?list=PLrYfgSbGP4qRsKnc-47wkxgz6ww1HMHox

The study was supported by the European Union projects MARBIGEN (FP7-REGPOT-2010-1) and ViBRANT (RI-261532)

Original Source:

Faulwetter S, Vasileiadou A, Kouratoras M, Dailianis T, Arvanitidis C (2013) Micro-computed tomography: Introducing new dimensions to taxonomy. ZooKeys 263: 1-45. doi: 10.3897/zookeys.263.4261