Thursday, May 28, 2015

6th International Barcode of Life Conference Early Registration Deadline extended

In case you haven't heard already through other sources: The deadline for early registration at the 6th International Barcode of Life Conference has been extended to June 15th, to allow more time for those awaiting the results of the abstract selection process to take advantage of the early registration fees. If you haven’t already registered for the conference you can find more information here.



Wednesday, May 27, 2015

Discoveries of the week #39

Brochopeltis mjoebergi Verhoeff, 1924 is redescribed from type and new material, a lectotype is designated and B. mjoebergi queenslandica Verhoeff, 1924 is synonymised with B. mjoebergi. B. mediolocus sp. n. is the first native paradoxosomatid described from Australia’s Northern Territory.

A new species of the order Polydesmida (flat-backed millipedes) which is the largest order of millipedes with about 3,500 species that also includes the millipede species that are known to produce hydrogen cyanide.
no DNA Barcodes


Comidoblemmus sororius, Comidoblemmus excavatus
Two new species of Comidoblemmus Storozhenko & Paik, 2009 are described and illustrated, C. sororius sp. n. (CHINA, Zhejiang) and C. excavatus sp. n. (CHINA, Guizhou). A key and a distribution map of all species in the world are presented.

The genus Comidoblemmus is a fairly new one, described in 2009. Until now it contained only one species, Comidoblemmus  nipponensis, widely distributed in Japan, Korea and Taiwan. Both species names refer to morphological characteristics.
no DNA Barcodes


Anteon huettingeri
A new species of Anteon Jurine, 1807 is described from Thailand, Nan Province: A. huettingeri sp. n. Morphologically the new species is similar to A. borneanum Olmi, 1984, A. jurineanum Latreille, 1809, A. insertum Olmi, 1991, A. yasumatsui Olmi, 1984, A. sarawaki Olmi, 1984, A. thai Olmi, 1984 and A. krombeini Olmi, 1984, but it is clearly different for the numerous sensorial processes present on the inner side of the paramere; these processes are absent in the other above species. Published identification keys to the Oriental species of Anteon are modified to include the new species.

These little Hymenoptera are actually parasitoids of leafhoppers, planthoppers and treehoppers and as such candidates for biocontrol. This new species from Thailand was named after its  collector, Dr Ernst Hüttinger.
no DNA Barcodes


Crematogaster erectepilosa, Crematogaster gullukdagensis
Crematogaster (Crematogaster) jehovae var. cypria Santschi, 1930 is raised to species rank. Two new, related species are described from the north-eastern part of the Mediterranean Basin: Crematogaster (Crematogaster) erectepilosa sp. n. (Dodecanese, Greece) and Crematogaster (Crematogaster) gullukdagensis sp. n. (Antalya Prov., Turkey). These three species are well distinguished from other species of the subgenus Crematogaster of the north-eastern part of the Mediterranean Basin in their first gastral tergite bearing numerous erect setae. Colour photographs of all taxa are provided, a key to the species of Crematogaster cypria group and species groups of the Crematogaster s. str. from the north-eastern Mediterranean region are given and a list of Crematogaster s. str. described from this region is provided.

The two new ant species have been named either after some erect setae on the antennal scape and after the type locality, the Güllük Dag mountains in the Antalya Province of Turkey.
no DNA Barcodes


Triplocania bravoi, Triplocania erwini, Triplocania trifida, Triplocania lamasoides
Four species of Triplocania, three with M3 simple, based on male specimens and one with forewing M3 forked, based on male and female specimens, are here described and illustrated, namely: Triplocania bravoi sp. n. (Napo: Ecuador), Triplocania erwini sp. n. (Napo: Ecuador), Triplocania trifida sp. n. (Mato Grosso and Rondônia: Brazil) and Triplocania lamasoides sp. n. (Rondônia: Brazil). They differ from all the other species in the genus, in which the males are known, by the hypandrium and phallosome structures. The female is first described for the M3 forked group. The identification key for males of the M3 forked group is updated.

More booklice species, this time from Brazil and Ecuador. Two species are named after fellow scientists (T. bravoi, T. erwini), and two after some morphological features and similarities to other species.
no DNA Barcodes


Putterlickia neglecta
Putterlickia neglecta, a new species here described and illustrated, is known from South Africa (Mpumalanga and northeastern KwaZulu-Natal), Swaziland and southern Mozambique. It is considered a near-endemic to the Maputaland Centre of Endemism. Plants grow as a shrub or small tree in savanna and thicket, or in the understory of inland, coastal and dune forests. Vegetatively it superficially resembles P. verrucosa, the species with which it has hitherto most often been confused.
Both species have stems with prominently raised lenticels, but P. neglecta differs from P. verrucosa in having sessile to subsessile leaves with mostly entire, revolute leaf margins, flowers borne on pedicels 8–15 mm long, with petals up to 6 mm long and spreading or slightly recurved. Putterlickia verrucosa has leaves with distinct petioles, spinulose-denticulate margins, much smaller flowers borne on pedicels up to 4 mm long, with petals up to 2 mm long and erect or slightly spreading. The relatively large flowers of P. neglecta resemble those of P. pyracantha, but the latter differs in having stems with obscure or sunken lenticels, leaf margins entire or spinulose-denticulate and inflorescence axes as well as pedicels usually reddish. A comparative table to distinguish among the five currently recognized species of Putterlickia is provided.

The species name refers to the fact that this particular species has for a long time been overlooked.
no DNA Barcodes



Tuesday, May 26, 2015

Not just paper parks

Aichi target 11 of the Convention of Biological Diversity promotes the expansion of the global protected area network to cover 17 percent of all terrestrial land and ­10 percent of coastal and marine areas by 2020.

At the recent World Parks Congress organized by the International Union for the Conservation of Nature (IUCN) in Sydney, Australia, conservation professionals drafted twelve innovative approaches, as part of the 'Promise of Sydney', to help transform decision-making, policy, capacity and financing for protected areas in the next decade. The document includes a list of 20 important recommendations to help reach global conservation goals. Many of the recommendations are provided for single countries to take action individually. 


It has been shown that working at the country level is less efficient than promoting transnational collaborations. As a result, platforms that support international collaborations from planning based on improved data to effective management should be strengthened.

They also state that mechanisms for international collaboration should be in place and strengthened quickly, as global change and other threats are quickly eroding biodiversity. Collaborations are crucial in specific key areas, e.g. more data are needed on the distribution of species, particularly for plants and for less known groups such as invertebrates. Creating and maintaining the core data resources should also be secured. The researchers also state that the current protected area network is biased towards higher lands and unproductive landscapes, missing many priority areas for conservation. As such, many species are currently not protected.

There should also be an emphasis on protecting all species that are currently unprotected globally. Meeting a percentage target of protected area coverage within individual countries is not enough. In addition, the international community should ensure that resources are available to effectively manage protected areas once they are established.

Protected areas are the cornerstone of biodiversity conservation. However, maintaining biodiversity values in the future—by mitigating the negative impacts of threats—requires effective protected area management. The information needed to assess management effectiveness is missing from most protected areas. A recent assessment on a very limited number of protected areas, for example, concluded that only 24 percent had sound management. The main limitations to the effective management of protected areas arise from the lack of financial resources (especially in developing countries) or deficiencies in management (e.g., lack of skilled staff). As a result, international donors should increase funding for protected area management in developing countries, where financial resources are scarcer. Funding could also be ­generated through the development of innovative financial mechanisms (e.g., ­biobanking or ­conservation easements) on private and community-owned land. Enhanced national and international collaborations in capacity-development activities should also be promoted as a means of sharing the best management practice experience in order to support protected area managers. This would help managers better involve local stakeholders in management decisions and develop appropriate responses to changes in threats.


Monday, May 25, 2015

sedaDNA

Do you want to learn about another interesting application of metabarcoding? If so, keep reading:

Paleoenvironmental studies are essential to understand biodiversity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes.

The idea is that organismal DNA can be directly obtained from recent and past sediments even in the absence of visible fossils. The development of metabarcoding methods now allows massive sequencing of ancient DNA contained in such sedimentary archives. Reconstructions of ancient environments often rely on indicator taxa which requires expert knowledge, but quantitative ecological analyses through direct sequencing of environmental DNA might provide more objective information. 

A new study by a group of French colleagues reports on the use of sedaDNA to investigate plant community changes in the catchment of Lake Anterne in the northern French Alps (2063m above sea level) over the last 6400 years. 

Multivariate analysis of ecological communities is a powerful tool that allows an objective understanding of the processes determining environmental variation (Legendre & Legendre 2012), but they have seldom been applied to sedaDNA data. In this study, we combined these two approaches, using metabarcoding data from a subalpine lake, along with data on present plant species assemblages. Our purpose was to infer past vegetation dynamics in the catchment during the Holocene, and to assess the relative importance of human impacts, natural evolution of communities and variation in climatic conditions in the observed trajectories.

The study provided some in-depth insight into the recent history of plant communities and the extend of human impact. The authors conclude that subalpine pine forests and tall-herb communities were the dominant vegetation in the lake catchment before human arrival. An indicator for a this is a change to taxa from open environments, typically subalpine meadows which is the result of grazing by cattle or sheep. Indeed DNA analyses have proven the presence of cattle and/or sheep herds in the Lake Anterne catchment during the late Iron Age and the Roman period, as well as during the Middle Ages and the Modern Times.

The sedaDNA-based approach currently has some limitations but offers, in addition to a relatively fast and easy protocol, some interesting perspectives. In this study, only sequences with a perfect assignment score (100%) were considered; consequently, data were highly dependent on the completeness of the reference database. In addition, the taxonomic resolution of the trnL P6 loop does not always allow identification to the species level, with barcodes often shared by several species. However, this fragment represents only a very limited part of the chloroplast DNA, less than one-one-thousandth of the whole molecule. The fact that such a small part of the chloroplast DNA can be reliably amplified demonstrates that a very large number of chloroplast DNA fragments are present in the DNA extract, and thus in the core slice. The next challenge will be to more efficiently extract the taxonomic information from those DNA fragments contained in the core. One possibility might be to directly sequence the DNA extracts using a shotgun approach (Taberlet et al. 2012c; Zhou et al. 2013). An ongoing project exists to sequence the whole chloroplast genome for approximately 4500 species of alpine flora. Shotgun sequencing combined with the availability of an exhaustive reference database containing the entire chloroplast DNA molecules creates the potential for a much more precise reconstruction of past plant communities, with identifications to the species level, and opens unprecedented avenues in paleoecology.

Friday, May 22, 2015

The Top 10 Species of 2015

The top 10 species list is out! This list is compiled annually by the SUNY College of Environmental Science and Forestry, International Institute for Species Exploration. The institute's international committee of taxonomists selected the Top 10 from among the approximately 18,000 new species named during the previous year. They released this year's list May 21 to recognize the birthday, May 23, of Carolus Linnaeus, father of modern taxonomy. The annual list, established in 2008, calls attention to discoveries that are made even as species are going extinct faster than they are being identified.

Feathered Dinosaur: 'Chicken from Hell' Anzu wyliei 
With a mixture of bird and dinosaur features, Anzu wyliei is from a bird-like group of dinosaurs that lived in North America. A contemporary of the more famous T. rex and Triceratops, this species made nests and sat on the eggs until they hatched. Among their bird-like features were feathers, hollow bones and a short snout with a parrot-like beak. These omnivores appear to have lived on floodplains eating vegetation, small animals and possibly eggs. Three well-preserved partial skeletons were discovered in North and South Dakota, in the Hell Creek Formation. Because some caenagnathids were chicken-sized, this new dinosaur was dubbed "chicken from Hell." However, at more than 10 feet in length (3.5m), 5 feet in height (1.5m) and 600 pounds (200-300kg), this was no chicken.

Coral Plant: Balanophora coralliformis 

This parasitic plant, discovered and almost immediately considered endangered, has elongated, repeatedly branching, and rough-textured aboveground tubers. These peculiar tubers give this root parasite from the Philippines a coral-like appearance distinct from the more typical underground tubers of related species. Parasitic plants do not contain chlorophyll and are incapable of photosynthesis, so they draw their nutrition from other living plants. This species is, so far, known from fewer than 50 plants, all found between 4,800 and 5,600 feet (1,465 and 1,735 m) elevation on the southwestern slopes of Mt. Mingan in mossy forest areas. Because so few plants are known to exist, and the narrow area in which they live is unprotected, the scientists who described it consider the plant critically endangered.

Cartwheeling Spider: Cebrennus rechenbergi 
This agile arachnid from the desert uses a gymnast's trick to escape from threatening situations: It cartwheels its way out of danger. When danger comes calling, the spider first assumes a threatening posture. If the danger persists, the spider runs and, about half the time that running turns into cartwheeling which is twice as fast. Terrain is not a challenge: the spider can spin across flat ground as well as up and down hills. Rather than attempting to cartwheel away, the spider propels itself toward the source of the threat, perhaps invoking the theory that the best defense is a good offense. In the barren sand dunes where the spider lives, running away can prove pointless because there is no place to hide. The high temperatures of its desert habitat would be fatal to the spider if it persisted in this high-energy routine for long, so cartwheeling is thought to be an escape option of last resort. Even before the spider had been officially named, its behavior inspired a biomimetic robot that can similarly walk or roll.

The X-Phyla: Dendrogramma enigmatica 

Dendrogramma enigmatica and a second new species, D. discoids, are multicellular animals that look rather like mushrooms, with a mouth at the end of the "stem" and the other end in the form of a flattened disc. The best information suggests that they are related to the phylum Cnidaria (jellyfish, corals, sea anemones and hydras) or Ctenophora (comb jellies) or both, but the new animals lack evolutionary novelties unique to either and could be an entirely new phylum. They also resemble fossils from Precambrian time, perhaps making them living fossils of sorts. The mystery surrounding this animal accounts for its name, and its relationships are likely to remain enigmatic until specimens can be collected suitable for DNA analysis. The new animal is small, with a stalk less than a third of an inch (8 mm) in length and a "cap" that measures less than a half-inch (11mm) across. It was found on the sea floor, at a depth of about 3,200 feet (1,000 meters), off Point Hicks, Victoria.

Bone-house Wasp: Deuteragenia ossarium 

This insect, which tops out at about a half-inch (15mm) in length, has a unique way to protect its offspring. The wasp constructs nests in hollow stems with several cells, each separated by soil walls. The wasp kills and deposits one spider in each cell to provide nourishment for her developing young. Once her egg is laid, she seals off the cell and hunts a spider for the next cell. Rather than provisioning the final or vestibule cell with a spider, she fills it with as many as 13 bodies of dead ants, thus creating a chemical barrier to the nest. This is the first animal known to take this approach to securing the front door to a nest. This species, found in Gutianshan National Nature Reserve in eastern China, has significantly lower parasitism rates than similar cavity-nesting wasps. Camouflage is supplied by a veil of volatile chemicals emitted by the dead ants, thwarting enemies that hunt wasp larvae by scent.

Indonesian Frog: Limnonectes larvaepartus 

There's an exception to every rule and the newest species of fanged frog is such an exception. Unlike other frogs, Limnonectes larvaepartus from Sulawesi Island, Indonesia, gives birth to tadpoles that are deposited in pools of water. On one occasion, a female gave birth to a tadpole in the hand of a scientist at the moment she was captured. Fewer than a dozen of the world's 6,455 frog species have internal fertilization and all except this new species lay fertilized eggs or give birth to tiny froglets. The species, about 1.5 inches long (40mm), is found in the island's Northern Peninsula on the western edge of the Central Core. The region has not been fully explored for frogs, so the extent of this species' range is not yet known. The frogs live in natural and disturbed forest habitats, often in areas occupied by one to five other species of the same genus. The frogs are found above flowing streams in leaf litter, grassy vegetation, or on rocky substrates.

Walking Stick: Phryganistria tamdaoensis 

While this new stick insect is not the world's longest, it belongs to a family known as giant sticks. At 9 inches in length, Phryganistria tamdaeoensis is compelling evidence that, in spite of their size, more giant sticks remain to be discovered and our knowledge of these masters of camouflage is far from complete. This giant stick is common in the town of Tam Dao visited by many entomologists, yet it escaped notice until now. If you would like to see one of these big bugs up close, you are in luck. Living specimens are on display at the vivarium of the Royal Belgian Institute of Natural Sciences in Brussels. The newcomer gets its name from the beautiful Tam Dao National Park in a mountainous area in the northwestern part of Vietnam. By the way, the record is held by Chan's megastick, Phobaeticus chani, at more than 22 inches (567 mm), named in 2008 from Borneo.

Sea Slug: Phyllodesmium acanthorhinum 

For this sea slug, the Top 10 competition was more than a beauty contest. It is a "missing link" between sea slugs that feed on hydroids and those specializing on corals. Gastropods do not get more photogenic than sea slugs whose graceful lines and vivid coloration make them beauties of the deep. This new species, which photographs in shades of blue, red and gold, also contributed to a better understanding of the origin of an unusual symbiosis in other species of the genus. Related sea slugs have multi-branched guts in which algae called zooanthellae live. These algae have a primary symbiotic relationship with the corals on which the sea slugs feed. Once sequestered in the gut, the photosynthetic algae produce nutrients of benefit to the host. The newly identified species is an inch long, more or less (17-28 mm), and resides in the Japanese islands.

Bromeliad: Tillandsia religiosa 

During Christmas celebrations in Mexico, elaborate altar scenes or "nacimientos" depicting the birth of Christ are assembled by villagers. In Sierra de Tepoztlán, Tlayacapan, San José de los Laureles, and Tepoztlán, a beautiful bromeliad plant is frequently incorporated in the display. The plant turned out to be new to science. Tillandsia religiosa, with its rose-colored spikes and flat green leaves, can be found growing up to 5 feet tall (1.5m) in rocky habitat in northern regions of Morelos, Mexico. Stemless, solitary plants are found on cliffs and vertical walls in deciduous, coniferous, oak and cloud forests at altitudes between 6,000 and 7,000 feet (1,800 to 2,100 m) elevation, where they flower from December to March. The bromeliad is an example of a species long known to local inhabitants but only recently discovered by science.

Pufferfish: Torquigener albomaculosus

Scientists recently solved a 20-year-old mystery under the sea and discovered a new fish. Intricate circles with geometric designs about six feet (2 meters) in diameter, found on the seafloor off the coast of Amami-Ōshima Island, were as weird and unexplained as crop circles. They turn out to be the work of a new species of pufferfish, Torquigener albomaculosus. Males construct these circles as spawning nests by swimming and wriggling in the seafloor sand. The nests, used only once, are made to attract females. The nests have double edges and radiating troughs in a spoke-like geometry. The design isn't just for show. Scientists discovered the ridges and grooves of the circle serve to minimize ocean current at the center of the nest. This protects the eggs from the turbulent waters and possibly predators too. Yoji Okata, an underwater photographer, first observed the artistic behavior. Subsequently, a team of ichthyologists and a television crew carried out an expedition to record the phenomenon.

By the way, none of the species has been barcoded.

Wednesday, May 20, 2015

Great Nature Project

You might have heard about this and came across some ads but in case not, here is the sales pitch:

National Geographic’s Great Nature Project is an initiative that inspires people to explore nature, take pictures of living things, and share their observations with the world at greatnatureproject.org. Anyone, anywhere in the world with access to a camera and the internet can contribute to the Great Nature Project at any time at greatnatureproject.org. From May 15 to 25, 2015, we especially encourage everyone to get outside and share photos of their encounters with plants, animals, and fungi as part of a global snapshot of biodiversity. The goal of the global snapshot is to document biodiversity all over the world during a specific window of time, repeated annually. Over time, this will provide data that can be used to answer scientific questions and provide useful information to decision-makers. 

The Great Nature Project website is integrated with iNaturalist.org to record observations in a standardized way and allow other users to comment on and suggest species identifications for observations. Participants can also contribute to the global snapshot of biodiversity using mobile apps created by iNaturalist, including apps in Spanish.

You can think of the Great Nature Project as a global bioblitz and if for some reason you can't get outside to make observations and photos yourself, you can help identify what others saw by adding comments and identifications. The iNaturalist site has excellent tools for finding observations from places and taxa of interest. Some 454 000 photos have been uploaded so far from a lot of places around the globe. Keep them coming, still five more days to go.

Tuesday, May 19, 2015

Barcoding Medicinal Plants

A plant which has been used for medical purposes at one time or another, and which, although not necessarily a product or available for marketing, is the original material of herbal medicines.
Definition of the term "Medicinal Plants", WHO

The global market of products derived from plants is estimated at $83 billion US and continues to grow. Furthermore, it is estimated that approximately 25% of modern drugs are derived from plant products. According to the WHO, between 65% and 80% of the populations of developing countries use medicinal plants as remedies and this number is also steadily growing. 

More and more medicinal plant products are produced for the global market and companies seek clinical trials to market their products e.g. as drugs in U.S. and European markets. Therefore, the authentication of the ingredients is becoming a critical, international issue. Mis-identification and adulteration of herbal remedies needs to be monitored and addressed. In a guest post in this blog a colleague from Nigeria provided a local example of the problems agencies are facing worldwide.

A new study published in PLoSONE shows another piece of this truly global puzzle. A group of researchers from Brazil used DNA barcoding (matK, rbcL and ITS2 regions) as well as qualitative and quantitative chemical analyses to confirm the identity of selected products. The colleagues studied eight species approved by the WHO for the production of medicinal herbs and sold in Brazilian markets:
Hamamelis (Hamamelis virginiana)
Chamomile (Matricaria recutita)
Espinheira Santa (Maytenus ilicifolia)
Guaco (Mikania glomerata)
Asian Ginseng (Panax ginseng)
Passion flower (Passiflora incarnata)
Boldo-do-Chile (Peumus boldus)
Valerian (Valeriana officinalis)

The results of the study are interesting but also a bit alarming as the level of substitutions may be as high as 71%. Using qualitative and quantitative chemical analyses, this study identified situations in which the correct species was being sold, but the chemical compounds were not present. Even more troubling, some samples identified as substitutions using DNA barcoding contained the chemical compounds from the correct species at the minimum required concentration. This last situation may lead to the use of unknown species or species whose safety for human consumption remains unknown.

This shows the true power of this combined approach showing that it is possible for a sample to pass quality control tests even if it does not belong to the correct species and at the same time that there are correctly identified products that don't contain sufficient amounts of chemically active compounds. The authors conclude:

The present study showed a great number of species substitutions and mislabeling, demonstrating that the current surveillance methods are not being efficient to control he herbal medicine market. Also, we showed that the traditional methodologies of species identification using chemical analysis are, in the majority of cases, not adequate to correctly identify a plant species. Thus, we propose the use of DNA barcode as a powerful first screening step. Applying the DNA barcode technique to the quality control of herbal medicine production will make the process safer, more reliable, and cheaper because substitutions will be promptly discarded without requiring more expensive chemical analyses that are otherwise necessary.