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Inspired by eLife, Pensoft now deposits article XMLs on GitHub

A core principle at Pensoft Publishers is openness – all of our journals are Open Access and available in multiple formats (both human-readable, e.g. PDF and semantically enhanced HTML, and machine-readable, such as XML) to simplify re-use of information and advance scientific research.

In accordance with this philosophy and starting Mon, 15/07/2013, the XML of all articles in ZooKeys, PhytoKeys and MycoKeys are now available on GitHub for all to see, comment, suggest changes and more.

At Pensoft, a guiding principle is technological excellence – we use the best tools available (and build new ones when existing ones are lacking) to provide a service that is advanced, yet easy and accessible. GitHub can be described as a social platform and network used mostly by software developers for coding, discussing, changing, and keeping track of all that. A major benefit of re-use is that it acts as an additional check for quality. As programmers say “given enough eyeballs, all bugs are shallow”.

“We have been impressed by the innovative approach of the eLife journal to use GitHub as a repository for their article XMLs and quickly followed it by advice of Prof. Roderic Page from the University of Glasgow. In a blog post, he pointed out how small errors in the markup of citations could prevent linking those citations to their online versions. Certainly the way to go to turn academic publishing into a more socially based enterprise!” said Prof. Lyubomir Penev, managing director of Pensoft.

Posting of the article XMLs on GitHub would allow these to be corrected and corrections/comments to be submitted through the repository feedback functionality, the so called “pull requests”. Moreover, all changes to the original version can be tracked in public. A good use case didn’t wait for long. Prof. Page wrote a script that identifies literature references lacking DOIs, then automatically checks CrossRef and yields back the missing DOIs. It will be straightforward to insert the missing DOIs into the article XMLs and to expose the version history.

Researchers described a new species of Noctuidae moth from Iran which is the fifth described species of the genus Anagnorisma. The new species A. chamrani has its name in honour of Dr. Mostafa Chamran (1932–1981), an Iranian scientist and defence minister. The study was published in the open access journal Zookeys.

During an expedition at high altitude of above 2500 m of north-eastern Iran on a cold night in late summer 2012, a couple of undescribed specimens of Anagnorisma moths were collected. The specimens had been attracted to an ultraviolet light trap on the Binaloud Mountain near Mashhad city, the capital of the Khorasan-e-Razavi province of Iran. They have a wingspan of 34-35 mm. The new species was collected in a narrow river valley dominated by mountain sainfoin (Onobrychis cornuta), wild almond (Prunus (Amygdalus) scoparia), and downy brome (Bromus tectorum).

A. chamrani is the sister species of A. eucratides, which is only known from eastern Afghanistan at altitudes of 2050 to 2450 m of the Hindu Kush Mountains. A. eucratides is the most similar species to chamrani in the wing pattern, external and genitalia characteristics and it is also the closest geographically.

Owlet moths (family Noctuidae) are a large worldwide group of more than 20,000 species of nocturnal lepidopterans, attracted to lights and mostly have dull protective coloration, although some exceptions occur. Most adults feed on fruits, sap, nectar, or other sweet fluids. The larvae vary considerably in size, and range from dull to colourful and from smooth to hairy. Many species feed on foliage and seeds, whereas others bore through stems and fruits. Larvae of some species are known as cutworms and live in the soil near the soil surface, and they bite off young plants just above ground level at night.

Original source:

Gyulai P, Rabieh MM, Seraj AA, Ronkay L, Esfandiari M (2013) Anagnorisma chamrani sp. n. (Lepidoptera, Noctuidae) from Iran. ZooKeys 317: 17–25. doi: 10.3897/zookeys.317.551

After nearly 25 years of searching, three scientists have finally found Waldo. No, not the loveable bespectacled character in children’s picture books, but rather an unusual clam discovered off the coast of California and British Columbia.

Paul Valentich-Scott from the Santa Barbara Museum of Natural History, and Diarmaid Ó Foighil from the University of Michigan, Museum of Zoology first began discussing this unusual clam back in 1989. Valentich-Scott discovered his strange specimens off the coast of Santa Barbara and Morro Bay, California, while Ó Foighil uncovered his while trawling for invertebrates off Vancouver Island, British Columbia.

At a scientific conference Valentich-Scott and Ó Foighil were chatting about clams during a break in the proceedings. As they were discussing new discoveries, the light went off. They had discovered the same new species, at the same time, but over 1,000 miles apart.

Neither scientist could identify the animal, and both were amazed by its thin, translucent shell and long willowy tentacles. Ó Foighil was able to collect and observe living specimens of the new species. ”We were looking closely at sea urchins and noticed something crawling on the fine spines covering the urchin body.”, declared Ó Foighil, ”We were amazed to see that there were minute clams crawling all over the sea urchin.”

Thus two decades of research began, trying to understand and formally describe this new animal. ”We never anticipated this would be such a long project.”, Valentich-Scott exclaimed, ”But every time we started in one direction we hit a wall and needed to begin again.”

Rescue finally came from doctoral student Jingchun Li at the University of Michigan, Ann Arbor. Li is a specialist in clam DNA. She was able to amplify the DNA of the new species and compare it to other similar species. ”We were pleased to see the new species was very distinct genetically.”, said Li, ” However we were surprised to find that its closest relative was from the South Atlantic Ocean off Argentina.” Valentich-Scott and Ó Foighil invited Li to collaborate on the final publication.

Valentich-Scott stated, ”This is a very peculiar animal, they only seems to live on the spines of one type of sea urchin in a commensal relationship. We found it ironic that the new species was in the genus Waldo and just couldn’t help but ask: “Where’s Waldo?”

Original source:

Where’s Waldo? A new commensal species, Waldo arthuri (Mollusca, Bivalvia, Galeommatidae), from the Northeastern Pacific Ocean. ZooKeys 316: 67–80, doi: 10.3897/zookeys.316.4256

 

Researchers from the University of Alaska Fairbanks (Derek Sikes and Jill Stockbridge) discovered a strange new insect on Prince of Wales Island, Alaska. It belongs to an enigmatic group that might help scientists understand the evolutionary origin of the Fleas. The new species belongs to the insect order Mecoptera which includes the scorpionflies, hangingflies, and snow scorpionflies. The description has been published recently in the open access journal ZooKeys.

“We process thousands of Alaskan insects specimens into our collections at the University of Alaska Museum every year so it’s rare that we see something that throws us for a loop. I called Derek, the Curator of Insects for the museum, into the lab and asked him what kind of insect this was and he didn’t even know the order!”, said co-author Jill Stockbridge.

With a digital photo in hand they posted the image on Facebook so their entomologist friends could offer their opinions. It’s such a strange insect that, not surprisingly, most suggestions were wrong. One entomologist, Michael Ivie, of Montana State University, recognized it as the genus Caurinus of which only one species, from Washington and Oregon, was previously known.

“In addition to being the second known species of such an usual group of insects, we were excited to learn from fossil evidence that these two species belong to a group that probably dates back over 145 million years, to the Jurassic!” said the lead author Derek Sikes.

These tiny (2 mm) flea-like animals feed on a leafy liverwort that grows in coastal forests. A video in which Loren Russell, the author of the first species and who joined the authors during a May 2013 expedition in Alaska, shows how to collect this new species is online at: https://vimeo.com/68819818 and a video showing this new species hopping is online at: https://vimeo.com/68819819 .

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Original Source:

Sikes DS, Stockbridge J (2013) Description of Caurinus tlagu, new species, from Prince of Wales Island, Alaska (Mecoptera, Boreidae, Caurininae). ZooKeys 316: 35. doi: 10.3897/zookeys.316.5400

 

Additional Information:

Funding for this research was provided by the Alaska Department of Fish and Game.

A new species of rare and beautiful plant has been described from the biodiversity rich Peninsular Malaysia. Ridleyandra chuana is endemic to the region and only known from two small montane forest populations. The conservation status of this recently described delicate flower is assessed as Endangered due to its restricted distribution. The new species was described and illustrated in the open access journal PhytoKeys.

Ridleyandra chuana is a perennial herb with a woody usually unbranched stem crowned by an asymmetrical rosette of dark green leaves covered in fine hairs. The beautiful and delicate cone-like flowers are white with dark maroon purple stripes. They rarely appear in more than two in one go usually flowering in succession. Ridleyandra chuana grows on moss-covered granite rock embedded in soil or on low moss-covered granite boulders, in extremely damp, deeply shaded conditions on steep slopes in valleys.

Although the species is only formally described now, it was in fact first encountered as early as 1932 at Fraser’s Hill, Pahang. However, it was only in 1999 when another population was discovered by L.S.L. Chua on Gunung Ulu Kali, Pahang, that sufficient material was available for its description. Since then, both these localities have been revisited and the Gunung Ulu Kali population is now the focus of conservation.

The new species is named in honour of Dr. Lillian Swee Lian Chua, botanist and conservationist, who first discovered this species on Gunung Ulu Kali while making an ecological inventory of the summit flora. Under the IUCN criteria, this species is assessed as Endangered because it is known from two localities, one of which is threatened, and only 130 known individuals.

“The population at Fraser’s Hill falls within a Totally Protected Area and consists of about 30 plants that grow in an undisturbed site away from tourist trails and is too remote to be affected by development. The other population consists of less than 100 plants at Gunung Ulu Kali, which is on private land in a hill resort that is severely threatened by road widening and associated landslips, by changes in microclimate due to edge effect as the forest becomes more and more fragmented and that is in danger of encroachment from future development. The chances of this latter population surviving is very slim. On the other hand, the rediscovery of the Fraser’s Hill population after a hundred years illustrates the resilience of species to survive if the habitat remains undisturbed.”, explains Dr. Ruth Kiew, the author of this study.

Original Source:

Kiew E (2013) Ridleyandra chuana (Gesneriaceae), a new species from Peninsular Malaysia. PhytoKeys 25: 15. doi: 10.3897/phytokeys.25.5178

Scientists discovered a tiny new species of catfish in the waters of Rio Rio Paraíba do Sul basin, Brazil. The new species Pareiorhina hyptiorhachis belongs to a genus of armored catfishes native to South America where and found only in Brazil. These peculiar fish get their name from their strange elongated mouth barbels that remind of cat’s whiskers. The new species is distinguished from others species of the genus by the presence of a conspicuous ridge on the trunk posterior to the dorsal fin (postdorsal ridge). The description of the diminutive new species was published in the open access journal Zookeys.

Pareiorhina hyptiorhachis is only about 3-3.5 cm in length, making one of the smallest representatives of the catfish order. Although the new species is only the size of a decorative fish, there are even smaller representatives in the group. Some of the smallest species of Aspredinidae and Trichomycteridae for example reach sexual maturity at only 1 cm in total.

On the other side of the scale is the wels catfish whose representatives can reach more than 2.5 metres (8.2 ft) in length and sometimes exceeded 100 kilograms (220 lb). This fish has been also recorded to feed on frogs, rats, mice and even some aquatic birds. Many of the large catfish species are farmed or fished for food thus being of significant scientific importance. Small representatives, on the other hand, are often used as aquarium decorative fish.

Original Source:

Silva GSC, Roxo FF, Oliveira C (2013) Pareiorhina hyptiorhachis, a new catfish species from Rio Paraíba do Sul basin, southeastern Brazil (Siluriformes, Loricariidae). ZooKeys 315: 65. doi: 10.3897/zookeys.315.5307

The wasp family Platygastridae is a large group of tiny, exclusively parasitoid wasps distributed worldwide. The genera Odontacolus and Cyphacolus, belonging to this family, are among the most distinctive wasps because of the peculiar hump-like formation on the rear part of their bodies. Despite their intriguing body shape, the generic status of these two groups has remained unclear. A new extensive study published in the open access Zookeys presents a morphological phylogenetic analysis including an astonishing 32 new species.

The peculiar shape of the so called horn structure on the back of these wasps is believed to be linked to the ovipositor system of the species. Only between 1 to maximum 2.5 mm long, these tiny wasps are actually vicious parasitoids, using their ovipositor to inject eggs into spider eggs, thus ensuring the development of their offspring at the expense of other species.

Previously considered to be relatively rare based on material available in collections, recent intensive collecting using Malaise and yellow-pan traps has revealed that some species of Odontacolus are moderately common, leading to the description of 32 species from across Africa, Australia and Asia.

“This has been an intriguing study for several reasons; it has uncovered many new species of this group of wasps; their biology is particularly fascinating given they parasitise the eggs of spiders, and their horn like structure makes them very easy to identify.”, comments Professor Andy Austin.

Original Source:

Valerio AA, Austin AD, Masner L, Johnson NF (2013) Systematics of Old World Odontacolus Kieffer s.l. (Hymenoptera, Platygastridae s.l.): parasitoids of spider eggs. ZooKeys 314: 1. doi: 10.3897/zookeys.314.3475

The white toothed shrew genus Crocidura is known as the largest mammal genus, with more than 180 species distributed around the world. A recent genetic analysis of the white toothed shrew fauna of Vietnam revealed the misinterpretations of previous morphological studies of the species, including the description of a new species of these very small mammals. The study was published in the open access journal ZooKeys.

Describing new mammal species is an unusual event nowadays when mammal fauna has been by and large already thoroughly studied by zoologists during the previous centuries. Molecular analysis, however, presents an additional tool for the complex cases of morphological analysis, thus helping scientists to uncover previous mistakes, and even to find previously overlooked separate species.

The new species Crocidura sapaensis is a dark-grey and relatively small white toothed shrew, named after the Sa Pa District in Vietnam, where it was collected. During the study, the animals were found dwelling in a variety of the beautiful habitats in the vicinity of Tram Ton Station of Hoang Lien National Park, including mixed evergreen forest, banks of small streams and open grassy glades.

Previously confused with another species featured in this study (C. wuchihensis), the new species remained long unrecognized due to the great extent of morphological resemblance between the two. Judging solely by the looks, however, proved to be insufficient for the accurate recognition of species, with molecular analysis now offering scientists an opportunity to look under the surface.

“Our study concerns three species of Crocidura occurring in Vietnam, namely C. attenuata, C. tanakae and C. wuchihensis, and we came across an undescribed fourth species revealed by molecular analysis. While the molecular studies of Vietnamese material confirmed some of the results of the contemporaneous morphological studies, a number of anomalies were equally revealed, indicating the presence of several morphologically similar but molecularly distinct taxa.”, explains Paulina Jenkins, a zoologist at London’s Natural History Museum, about the horizons of the molecular analysis.

Original Source:

Jenkins PD, Abramov AV, Bannikova AA, Rozhnov VV (2013) Bones and genes: resolution problems in three Vietnamese species of Crocidura (Mammalia, Soricomorpha, Soricidae) and the description of an additional new species. ZooKeys 313: 61-79. doi: 10.3897/zookeys.313.4823

 

Notes to editors:

Winner of Best of the Best at the Museums and Heritage Awards 2013, the Natural History Museum welcomes more than five million visitors a year. It is also a world-leading science research center. Through its collections and scientific expertise it is helping to understand and maintain the diversity of our planet, with groundbreaking partnerships more than 70 countries around the world. For more information go to http://www.nhm.ac.uk

The new phase of the Encyclopedia of Life (EOL) Open Access Support Project (EOASP) is starting today, 1 July 2013, with some slight changes in eligibility criteria.

The aim of the EOASP project is to increase the data flow into EOL, promulgate the open access publishing model in taxonomy and support and educate the next generation of taxonomists in open science principles. It provides assistance for taxonomists living in developing countries to publish their results in quality journals and pays tribute to retired taxonomists by continuously supporting their research. EOASP is also an initiative aiming to motivate publishers to modernize their publishing models and workflows.

The main change in the eligibility criteria concerns the content of the publication. Manuscripts will be considered for funding only if they contain at least 4 taxon treatments; they do not need to be newly described taxa. A good example is a genus treatment (re-description) consisting of at least three species treatments, either new or re-described.

The total amount of funding per paper is increased to USD 500. The support for larger papers (e.g., larger revisionary works or monographs) will be limited to the same maximum of USD 500; authors should meet the remaining costs themselves. 

To read the new eligibility criteria or on our website please follow the link which is copied below: http://www.pensoft.net/page.php?P=29

A new species of the peculiarly shaped spoon worms has been recently discovered in Japan, and described in the open access journal Zookeys. These animals derive their name from their elongated and spoon-like projection (the proboscis), issuing from the barrel- or sweet potato-like roundish body proper (the trunk).

The new species Arhynchite hayaoi was discovered on a sandy tidal flat named Hachi-no-higata of the Seto Inland Sea, Japan. Like most spoon worms, the new species has the typical peculiar spoon shaped proboscis. The animal is of a pinkish-yellow colour, and its body length reaches about 10 cm in total.

Spoon worms, scientifically called Echiura, are a small group of exclusively marine animals. Although they are members of annelid worms, most of which has segmented structure, they have lost segmentation during their evolutionary history. Like the new species from Japan, most spoon worms live in shallow waters, but some are connected with deep sea waters. Most representatives are deposit feeders, which means that they use their “spoon” to collect organic particles or fragments from their surroundings.

Previously confused with a different species, the newly described spoon worm used to be in fact rather abundant and collected in great numbers from intertidal to subtidal sandy bottoms for fish bait in the Seto Inland Sea, Japan. Now that the true identity of the species is recognised, it seems to be in decline, with numbers dropping to a point where the spoon worm lost this economic importance.

Original Source:

Tanaka M, Nishikawa T (2013) A new species of the genus Arhynchite (Annelida, Echiura) from sandy flats of Japan, previously referred to as Thalassema owstoni Ikeda, 1904. ZooKeys 312: 13–21, doi: 10.3897/zookeys.312.5456.