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


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 Anyone, anywhere in the world with access to a camera and the internet can contribute to the Great Nature Project at any time at 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 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.

Thursday, May 14, 2015

Discoveries of the week #38

Kessleria cottiensis, Kessleria dimorpha, Kessleria alpmaritimae, Kessleria apenninica, Kessleria orobiae
The taxonomy of Kessleria, a highly specialized montane genus of Yponomeutidae with larval host restriction to Saxifragaceae and Celastraceae (Saxifraga spp. – subgenus Kessleria; Saxifraga spp. and Parnassia spp. – subgenus Hofmannia), is revised based on external morphology, genitalia and DNA barcodes. An integrative taxonomic approach supports the existence of 29 species in Europe (the two known species from Asia and North America are not treated herein). A full 658 bp fragment of COI was obtained from 135 specimens representing 24 species, a further seven sequences are >560 bp. Five new species are described: Kessleria cottiensis sp. n. (Prov. Torino, Italy; Dep. Hautes Alpes, France), Kessleria dimorpha sp. n. (Dep. Alpes-de-Haute-Provence, France), Kessleria alpmaritimae sp. n. (Dep. Alpes-Maritimes, France), Kessleria apenninica sp. n. (Prov. Rieti, Prov. L´Aquila, Italy), and Kessleria orobiae sp. n. (Prov. Bergamo, Italy).

Five new species of a genus with a highly specialized host-plant relationship with the plant family Saxifragaceae. Names refer to type localities with one exception (K. dimorpha) which refers to differences between females and males.
DNA Barcodes available

Edmockfordia calderonae, Edmockfordia saenzi
Two new species of Edmockfordia García Aldrete, from Valle del Cauca, Colombia, and the female of E. chiquibulensis García Aldrete, are described and illustrated. A key to the species of Edmockfordia is included; the genus was previously known only from Belize. The genus is re-diagnosed to include female characters. The distribution of the genus is considerably widened, from Belize to northeastern South America.

Two new species of booklice from Colombia. The authors honor two graduate students that helped collecting the specimens by naming the species after them. Pretty nice gesture that sets a precedent. Dear supervisors: here is a way of saying thank you to your students.
no DNA Barcodes

Potamonautes isimangaliso
A new species of freshwater crab, Potamonautes isimangaliso sp. n., is described from the western shores of False Bay, Hluhluwe, within the iSimangaliso Wetland Park, South Africa. While bearing a superficial resemblance to P. lividus, the new species has been found to be genetically distinct, diverging from the former by 7.4–7.8% in mtDNA. Potamonautes isimangaliso most closely resembles P. lividus, but is distinguished by a unique suite of carapace characters, colouration, and size. The new species also lives in close association with oxygen-poor, fresh ephemeral pans, while the habitat of P. lividus is well above the surface water line of the closest water body. An updated identification key for the Potamonautes species of South Africa is provided.

Another week with a new species of freshwater crab. This one is from South Africa. The species is named after the iSimangaliso Wetland Park, in KwaZulu-Natal where it was found.
no DNA Barcodes (although the paper refers to a COI sequence it cannot be accessed anywhere)

Meteorona kishinouyei
A new family, genus and species of cubozoan box jellyfish belonging to the order Chirodropida is reported from the eastern Japan. Meteorona kishinouyei gen. et sp. n. possesses the following unique morphological characters with respect to other known species in the Chirodropida: having one tentacle per scalpel-like unbranched pedalium and slightly raised unbranched gastric saccules. A comparative table of the primary diagnostic characters of genus and order in the Chirodropida is given. The order Chirodropida is redefined. The family Chiropsellidae is established. Discussion is provided on the implications for these findings on our current understanding of Cubozoan systematics.

Everything is new here, new species in a new genus in a new family. The genus name comes from the meteor-like appearance of the jellyfish shooting through the sea while swimming. The species is named after Professor Kamakichi Kishinouye.
no DNA Barcodes (only 18S rRNA)

Zachobiella yunanica
The genus Zachobiella Banks, 1920 is reviewed and a new species Zachobiella yunanica sp. n. described from China. All species found in China are redescribed, and Zachobiella submarginata Esben-Petersen, 1929 is recorded from China for the first time. A key to the adults of Zachobiella is provided.

A new brown lacewing species from the Chinese province Yunnan, hence the species name.
no DNA Barcodes

Goniothalamus flagellistylus
A new species, Goniothalamus flagellistylus Tagane & V. S. Dang, sp. nov. from Hon Ba Nature Reserve in Khanh Hoa Province, South Vietnam is described and illustrated. This species is most similar to Goniothalamus tortilipetalus M.R.Hend., but distinct in having 308–336 stamens (vs. ca. 170–260) and ca.120 carpels (vs. ca. 50–100) per flower, and Stigma and pseudostyles ca.8.5 mm (vs. 4–4.5 mm) long.

A new species of the custard apple family.  The species name is in reference to its flexuous styles.
DNA Barcodes available (rbcL and matK)

Wednesday, May 13, 2015

Map of Life

A new app was just released and it actually seems to be a very promising one. The idea is to allow people to check out local wildlife wherever they are in the world with the app telling them what species of animals and plants might be nearby.

Building on the Map of Life website, which provides a database of everything from bumblebees to trees, the app tells users in an instant which sets of species are likely to be found in their vicinity. Photos and text help users identify and learn more about what they see. The app also helps users create personal lists of observations and contribute those observations to scientific research and conservation efforts.

Map of Life assembles and integrates different sources of data describing species distributions worldwide. These data include species range maps, species occurrence points, ecoregions, and protected areas from providers like IUCN, WWF, GBIF, and more. All data assets are stored, managed, backed up, and accessed using a hosted cloud instance.

Thanks to a recording feature, citizen scientists everywhere can log their bird encounters and dragonfly sightings directly into the app and add to the biodiversity data available to scientists around the world. Making it easier and more globally streamlined for citizen scientists to contribute information is one of the key motivations behind creating the app. 

The world is changing rapidly and species continue to disappear before we even knew where they occurred, what role they had, and how we could conserve them. Too much of our knowledge is limited to too few places and species. Helping people everywhere to identify and then record biodiversity carries the potential to hugely extend the geographic and taxonomic reach of measuring the pulse of life.

The Map of Life app is available in six languages for iPhone and Android smartphones. I just installed it on my phone and after 10 minutes playing with it I can say it is really cool, fairly accurate and fun to work with. It is perfect for young citizen scientists, very accessible and easy to handle. Perfect for family outings, classroom excursions, even university courses.

The app puts a significant proportion of our global knowledge about biodiversity in the palm of your hand, and allows you to discover and connect with biodiversity in a place, wherever you are. Think of a field guide that continues to improve the more we all use it and add to it. That is the beauty of this mobile application, and its great strength.

My recommendation - get it, go out over the weekend and put it to the test, and don't forget to record and share your findings.

Tuesday, May 12, 2015

Introduction to DNA Barcoding - June/July course

Today, I'd like to take the opportunity to do some marketing for my DNA Barcoding Online Course. I haven't done that in a while :-) Here an excerpt from the course outline:

Introduction to DNA Barcoding

Course Description

Introduction to DNA Barcoding will provide students with a basic understanding of DNA-based approaches for species identification and discovery. Students will have the opportunity to explore the historical framework for species identification to learn why DNA Barcoding represents an advance. The program will then proceed into explorations of barcode workflows and culminate in an overview of applications. The course units will cover basic knowledge of genetics necessary to understand the method and the choice of particular molecular markers as standards for different taxonomic groups. This will also include a unit on analysis and interpretation of results. Several units will showcase the different applications of DNA Barcoding with a focus on socio-economic issues. Furthermore, the benefits for basic research especially in the fields of taxonomy, ecology, and evolution will be explored.

Learning Outcomes

At the end of this course students should be able to:

  • Describe and comprehend the genetic background of DNA Barcoding, and evaluate potential technical challenges.
  • Identify species by performing data base queries with common databases and interpretation of results.
  • Critically evaluate studies that utilized DNA-based taxonomy.
  • Develop skills to make informed decisions about molecular marker choice and laboratory needs.
  • Synthesize knowledge and effectively communicate about DNA Barcoding for grant proposals and interaction with policy makers.
Interested? Sign up and be part of an 8-week course that attracts students from different places of the world.

Monday, May 11, 2015

Barcoding local - Contributions by course participants (7)

Happy Monday. Today a guest post by Mailyn Gonzalez from the Instituto de Investigación de Recursos Biológicos Alexander von Humboldt in Bogotá, Colombia. She participated at the last Introduction to DNA Barcoding course and here is her take on barcoding in her home country:

Golden poison frog (image by Wilfried Berns)
Colombia is among the most biodiverse countries in the world. Major threats to our biodiversity are due to deforestation mainly driven by mining, urban expansion, industrial farming and illegal crops. In the last five years our economy seems to rely mostly on the energy industry with multiples projects to build hydroelectric power stations as well as oil and gold mining. However, other pressures such as species overexploitation and species invasions are also recognized to be a major problem even if better quantification of these issues is required.

In Colombia we have a strong taxonomic community that is continuously discovering and describing new species for science. In contrast, molecular disciplines have advanced slowly because of costs and legislation. Recently, more scientists are integrating molecular information into their research even if financial support remains a major obstacle.

Our institute's mission is to promote, coordinate and do research that contributes to the sustainable development of Colombia. DNA barcoding is a research line that I believe constitutes a valuable tool in facing important issues of conservation in my country. I will describe two particular projects that I would like to address.

1. Overexploitation of species: for example, Colombia is home to around 1900 species of birds, a lot of them geographically restricted and some groups highly trafficked. When bird species are confiscated they are usually labeled as “hummingbird” or “parrot’. However there are 152 hummingbird and 52 parrot species recognized. Being able to provide a proper identification would be important for: (1) legal action against the dealer, (2) determination of the geographic region where the species should be reintroduced (3) assess the overexploitation of each species and focus on prevention. Building a DNA barcode library of the species most trafficked across the borders would be a major advance in conservation.

A difficulty encounter is that environmental authorities have strict protocols of custody chain and normally do not rely systematically in the opinion of scientific experts. It is frustrating that so far they do not use the information being generated in major repositories. It would be challenging but fruitful to coordinate at least a pilot project where DNA could be collected from bird samples confiscated and proved how more accurate information can address solutions to diminish illegal species commerce.

2. Biomonitoring of ecosystems: Hydroelectric power and mining are driving the current national economy. In the first case, limnologists periodically assess the taxonomic composition of  the water reservoirs, a task that may take several days for one sample. In the case of mining, usually the soil biota is the most affected and also the least known. How to control the recovery of soil biota communities after mining? Or the success of a restoration site? I think that barcoding water and soil samples would be the most reliable and cost efficient way to monitoring these systems.

A major impediment right now in Colombia is funding. Once that the companies understand that this technology is reliable and cost-efficient they will support it, but first we require funds to set up a pilot and show them the utility of this initiative.

Friday, May 8, 2015

Market prices in conservation

Credit Matilda Luk, Princeton University
The wildlife trade involves thousands of vertebrate species and now rivals habitat loss as an extinction driver in some regions. However, its impacts are poorly known because field monitoring of wild populations is expensive, localized, and requires specialized expertise.

Approximately one third of the world’s birds sourced from most of Earth's ecosystems are traded. A staggering 1.5 billion live ornamental fish are exported every year. Thousands of reptile and mammal species are marketed legally and illegally. The illegal wildlife trade alone is worth US$10 billion per year, the total retail value of ornamental fishes adds up to US$2.2. billion and so on. 

Wildlife trade affects thousands and thousands of species, yet for only a handful of species we have enough information to assess what effect continuous harvesting has on their populations. For the vast majority of species, we really don't know what impact wildlife trade is having. It is a silent killer. Species decimated by trade are not necessarily considered endangered. Nor does wildlife trade leave cleared forests or other obvious signs of destruction in its wake as activities such as mining or illegal logging often do.

Researchers from Princeton University thought of a different way to to gauge and perhaps halt the devastation of the wildlife trade on populations of prized animals. They found that species that are disappearing as a result of the pet trade can be identified by changes in their market prices and trade volumes. Increasing prices and decreasing availability could mean that wild populations are plummeting. 

The researchers studied open-air pet markets on the Indonesian island of Sumatra and found that bird species that increased in price but decreased in availability exhibited plummeting populations in the wild. The researchers examined bird-market data from 1987 to 2013, and surveyed local ornithologists and expert birdwatchers to confirm that wild populations of the species most prized as pets declined as their price went up and market availability decreased.

They conclude that a prolonged rise in price coupled with a slide in availability could indicate that a species is being wiped out by its popularity in the pet trade. Through regular pet-market monitoring, conservationists and governments could use this information as an early indicator that a particular species is in trouble. At that point, more sophisticated measures could be taken to monitor and protect that species' wild population.

Market monitoring can be done far more quickly and cheaply than field-based monitoring of wild populations, especially in developing tropical countries where fieldwork requires special expertise and can be difficult to conduct. Those countries usually host a large number of species and have big markets for pets, yet have lax-to-nonexistent monitoring and conservation programs. 

This study also highlights the pet trade as an emerging threat facing many birds and other wildlife, one that can act independently from other drivers of extinction such as habitat loss.

Thursday, May 7, 2015

Discoveries of the week #37

A new species, Cherax (Astaconephrops) pulcher sp. n., from Hoa Creek, close to the village Teminabuan in the southern-central part of the Kepala Burung (Vogelkop) Peninsula, West Papua, Indonesia, is described, figured and compared with the morphologically closest species, Cherax boesemani Lukhaup & Pekny, 2008.

New species of crayfish with a species named derived from the Latin word “pulcher” meaning beautiful, alluding to the colorful appearance of the species. 
no DNA Barcodes

Previous research of Bornean Micronectidae Jaczewski, 1924 (pygmy water boatmen) is summarized based on the data from the literature and recent work. All the Bornean micronectids belong to the genus Micronecta Kirkaldy, 1897. Descriptions or redescriptions and a key to the eight species, which have so far been found in Borneo are presented, namely M. decorata Lundblad, 1933, M. ludibunda Breddin, 1905, M. liewi sp. n., M. lakimi sp. n., M. lumutensis Chen, Nieser & Lansbury, 2008, M. skutalis Nieser & Chen, 1999, M. kymatista Nieser & Chen, 1999) and M. quadristrigata Breddin, 1905. The synonyms are indicated under each species. To facilitate identification, illustrations and habitus photos are provided. The faunistic components of Micronectidae in Borneo are discussed from a zoogeographic point of view.

Two new pygmy water boatmen species from Borneo. One species was named in honor of Dr. Thor Seng Liew (NBC Naturalis and Sabah University, Malaysia) and the second after Dr. Maklarin Lakim who help service organizing the expedition in which the new species were discovered.
no DNA Barcodes

The Russet Bush Warbler Locustella (previously Bradypterus) mandelli complex occurs in mountains in the eastern Himalayas, southern China, Vietnam, the Philippines, and Indonesia. The taxonomy has been debated, with one (L. seebohmi) to four (L. seebohmi, L. mandelli, L. montis and L. timorensis) species having been recognised. We used an integrative approach, incorporating analyses of morphology, vocalizations and a molecular marker, to re-evaluate species limits in the L. mandelli complex. We found that central Chinese L. mandelli differed from those from India through northern Southeast Asia to southeast China in plumage, morphometrics and song. All were easily classified by song, and (wing + culmen)/tail ratio overlapped only marginally. Both groups were reciprocally monophyletic in a mitochondrial cytochrome b (cytb) gene tree, with a mean divergence of 1.0 ± 0.2%. They were sympatric and mostly altitudinally segregated in the breeding season in southern Sichuan province. We found that the Mt Victoria (western Myanmar) population differed vocally from other L. mandelli, but no specimens are available. Taiwan Bush Warbler L. alishanensis was sister to the L. mandelli complex, with the most divergent song. Plumage, vocal and cytb evidence supported the distinctness of the south Vietnamese L. mandelli idonea. The Timor Bush Warbler L. timorensis, Javan Bush Warbler L. montis and Benguet Bush Warbler L. seebohmi differed distinctly in plumage, but among-population song variation in L. montis exceeded the differences between some populations of these taxa, and mean pairwise cytb divergences were only 0.5–0.9%. We also found that some L. montis populations differed morphologically.

This new bird, the Sichuan bush warbler, resides in five mountainous provinces in central China.It was named in honor of the late Cheng Tso-hsin, China's greatest ornithologist. Cheng, founder of the Peking Natural History Museum.
no DNA Barcodes (why cytb??????)

The taxonomy of Chamaedrilus glandulosus (Michaelsen, 1888) s. l., most commonly known previously as Cognettia glandulosa, is revised. A recent molecular systematic study has shown that this taxon harbours two cryptic, but genetically well separated lineages, each warranting species status. In this study these two lineages are scrutinized morphologically, on the basis of Michaelsen’s type material as well as newly collected specimens from Central and Northern Europe. Chamaedrilus glandulosus s. s. is redescribed and Ch. varisetosus sp. n. is recognized as new to science. The two species are morphologically very similar, differing mainly in size, but seem to prefer different habitats, with Ch. glandulosus being a larger aquatic species, and Ch. varisetosus being smaller and mainly found in moist to wet soil.

A new enchytraeid species named after the variation in numbers of chaetae in the lateral preclitellar bundles. 

Three new species of Ripipteryx Newman (Orthoptera: Tridactyloidea: Ripipterygidae) are described from Colombia; namely R. diegoi sp. n. (Forceps Group) and R. guacharoensis sp. n. (Marginipennis Group) from Parque Nacional Natural Cueva de los Guacharos in Huila, and R. gorgonaensis sp. n. (Crassicornis Group) from Parque Nacional Natural Gorgona in Cauca. Ripipteryx diegoi sp. n. is characterized by the antennae black with white spots on flagellomeres 3–7, male subgenital plate with median ridge forming a bilobed setose process, epiproct produced laterally near its base and phallic complex with virga thickened distally and not reaching beyond the membrane. Ripipteryx guacharoensis sp. n. is characterized by the antennae thick with white spots present dorsally on flagellomeres 1–4 and 8, epiproct narrow and triangular, uncus reduced and lacking a distal hook, phallic complex with a concave ventral plate and a dorsal elevation in the middle extended to the virga, and the virga itself with two small projections basally. Ripipteryx gorgonaensis sp. n. is characterized by the epiproct with a lateral notch, antennae with a white dorsal spot on flagellomere 1 and flagellomeres 4–7 entirely white. The antennal color pattern of R. gorgonaensis sp. n. strongly resembles that of R. atra but differs from the latter in the absence of any significant morphological modification of the flagellomeres.

Three new mudcricket species, one named after the father of the first author, and the two after their respective type localities.
no DNA Barcodes

Seventeen new species of the genus Eugenia
Seventeen new endemic species of the genus Eugenia L. (Myrtaceae) are proposed from Madagascar, including: E. andapae N. Snow, E. barriei N. Snow, E. bemangidiensis N. Snow, E. calciscopulorum N. Snow, E. delicatissima N. Snow, Callm. & Phillipson, E. echinulata N. Snow, E. gandhii N. Snow, E. hazonjia N. Snow, E. iantarensis N. Snow, E. malcomberi N. Snow, E. manomboensis N. Snow, E. obovatifolia N. Snow, E. ranomafana N. Snow & D. Turk, E. ravelonarivoi N. Snow & Callm., E. razakamalalae N. Snow & Callm., E. tiampoka N. Snow & Callm., and E. wilsoniana N. Snow, and one new combination, Eugenia richardii (Blume) N. Snow, Callm. & Phillipson is provided. Detailed descriptions, information on distribution and ecology, distribution maps, vernacular names (where known), digital images of types, comparisons to morphologically similar species. Preliminary assessment of IUCN risk of extinction and conservation recommendations are provided, including Vulnerable (4 species), Endangered (2 species), and Critically Endangered (4 species). Lectotpyes are designated for Eugenia hovarum H. Perrier, Eugenia nompa H. Perrier, and E. scottii H. Perrier respectively.

An impressive array of new species from Madagscar, all endemics.
no DNA Barcodes

Wednesday, May 6, 2015

Barcoding local - Contributions by course participants (6)

And another guest post by a course participant. Jemilah Aliyu Ibrahim is a Senior Research Fellow at the National Institute for Pharmaceutical Research and Development in Abuja, Nigeria. Her area of interest are the complexities of the family Loranthaceae (mistletoes) in Nigeria. She leads the Institute's herbarium where she carries out and supervises identification of plant specimens for researchers, students and agencies. In addition she also documents indigenous knowledge on the use of plants for treatment of diseases and aims to verify such claims with appropriate laboratory studies. 

The Loranthaceae (mistletoes) is a family of parasitic plants that pose a serious threat to plantations and tended plants and impinges seriously on the productivity and the economic return of the host plants. Despite this, mistletoes are also medicinally very important in the treatment of ailments such as mental conditions, sterility, skin diseases, rheumatism, chest conditions and urino-genital problems, hypertension, diabetes, etc.  In Nigeria, leaves of mistletoes are packageed as herbal tea for treatment of some of the ailments mentioned above. The fruits also serve as food to some pollinators. 

In Nigeria, Loranthaceae poses serious challenges because the names available for most of the plants go only down to genus level. Characters for delineation and delimitation are overlapping either between the genera or within species. Observations made of specimens in the field and in herbaria also revealed very conspicuous similarities in the floral or vegetative features of some of these species which have made identification difficult. This has led to a high rate of wrong specific names being applied in many publications in Nigeria. The majority of herbal medicine producers labels their mistletoe remedies as just ‘mistletoes’ without referring to the specific name due to inadequate knowledge of the identity of the parasite used in the preparation. 

The above issues necessitated a revision of the family in Nigeria. Issues identified in the study are as follows:
1. Fifteen mistletoe species occur in Nigeria. Out of the 15 species, 7 could only be traced back to herbarium specimens. Some species found in the literature were neither found in the field nor traced to any herbarium specimen thereby raising serious issues about the conservation status of the species. 
2. There are wide phenotypic variations among individuals of the same species collected from different hosts in the same locality or different localities. 
3. The specimens of Tapinanthus globiferus from north-central, north-east to north-west zones might likely be harboring cryptic lineages evidenced from some clear morphological features. 
4. Most research works published on the plants in peer reviewed journals is likely based on wrong identifications.

All the issues mentioned above could be addressed by using DNA barcoding. The occurrence of the 15 recorded species needs to be confirmed and they require further documentation (at least one of these species is endemic to Nigeria). Secondly, DNA barcoding can be employed for routine identification because morphological characters are confusing and misleading. This will reduce the high rate of mis-identification observed and cases of adulteration of herbal remedies  can be avoided or reduced. Regulatory agencies can also use DNA barcoding to monitor genuineness of such herbal products.  Finally, DNA barcoding can be employed to determine if cryptic species occur in the Tapinanthus globiferus complex. 

Difficulties that might impede the use of this technique is the high cost of field surveys to collect representative specimens and this cannot be carried out by an independent researcher who does not have any sufficient funds, unless DNA can be extracted from herbarium specimens. Facilities for such studies are scarce and when available, it is too expensive and the technical Know-how is also lacking. 

Finally, when the above predicaments can be overcome, which I know it will be soon, then DNA barcoding will be a tool to watch out for in solving the taxonomic problems of this very important and highly medicinal family of Loranthaceae in Nigeria. 

From the Inbox: MATI course in Innsbruck

University Course on Molecular Analysis of Trophic Interactions (MATI)

14th – 25th of September 2015, Innsbruck, Austria

Molecular approaches offer exciting possibilities to study trophic interactions. Within the last decade considerable progress has been made in DNA-based methodology to unravel who eats what including predator-prey, host-parasitoid and herbivore-plant interactions across ecosystems. This course provides a hands-on introduction to molecular trophic ecology and offers the opportunity to discuss how to best apply these methods to your own research project.

By completing this course module the participants will have achieved a general understanding of the concepts of DNA-based diagnostics. They will be able to apply and develop basic molecular assays with the focus on the analysis of trophic interactions.

Online Enrollment until 31st of July 2015.

Contact: Christina Brückl via email or phone: +43 512 507 96501

Tuesday, May 5, 2015

Barcoding local - Contributions by course participants (5)

Another guest post from one of the course participants. This time Kelsey Hoffmann. masters student at Winona State Univeristy in Minnesota who is doing research on parasites.

DNA barcoding will be a very useful tool for the research that I am doing at Winona State University. I am currently trying to identify parasites that I have found in bobcats and river otters from Wisconsin. Unfortunately, during the collection process, many of the parasites get damaged making it extremely difficult to get an exact identification. With most cestode (tapeworm) species that have been collected from the bobcats the only way to identify them morphologically is to have an undamaged scolex.
The scolices of two different species of tapeworm: T. solium (A) and T. saginata (B). The only thing differentiating these two species of tapeworms is if hooks are present on the anterior end. Unfortunately, scolices are very fragile and hooks can come off during the collection processes making identification using morphology difficult and inaccurate. Image taken from here.
The scolex is considered the “head” of the tapeworm and is what attaches to the intestinal wall of its
definitive host. They are very small and incredibly difficult to find within the digested material from an animals gastrointestinal tract. If they are recovered, they are usually in very poor condition, making an accurate identification of its species virtually impossible. The identification process, and any other research planned, for the parasites found in the Wisconsin bobcats has been put on hold as samples have been sent to other institutions, like the University of Helsinki in Finland, for identification. Having to send out samples for identification not only puts a temporary stop to the furthering of the research it also cost money. The way these parasites are preserved also posses a problem for identification. Once removed from the intestine all parasites are put into vials containing 70% ETOH, this helps to halt any degradation but it also dehydrates the specimens making them hard to identify, morphologically, at a later date. This is where having the ability to do DNA barcoding here in the lab at Winona State would be a beneficial tool. 

Currently, river otters (Lontra canadensis) from Wisconsin are being examined at Winona State for gastrointestinal parasites. The most prevalent types of infections found in the river otters thus far are Echinostoma species, Acanthocephala species, and Nematode (roundworm) species. Within each of the parasite groups the specimens that have been collected range in different size, color, and morphological features. For example, within the Echinostoma species there have been at least two visually different looking specimens collected. 

The anterior oral suckers of Echinostoma
 collected from Wisconsin river otter intestines
The two specimens of Echinostoma spp. collected have different anterior oral suckers and were also much different in size. These different morphological features seem to suggest that these two specimens are two different species of Echinostoma, however, it is possible that they could also be the same species but are at two different stages of development. Without having access to an expert taxonomist it is difficult to get an exact identification. Being able to preform the steps to get the DNA barcodes at Winona State University for any of the parasite specimens collected would help to answer these types of questions in an accurate at timely manner.

Having DNA barcoding in the arsenal of tools that could be used to identify very small, and at times microscopic, parasites would be beneficial to this research. I think it would be fairly simple to start doing DNA barcoding at Winona State as many of the things we need to perform it we already have available. 

Monday, May 4, 2015

How to construct a reference library of DNA barcodes?

One of the main activities of the DNA Barcoding community is to generate an open access library of reference barcode sequences which enables everyone with the ability to obtain sequence information
to identify specimens. Barcodes of unidentified specimens can be compared with reference barcodes to find the matching species.

For over ten years we have already generated almost 4 Million barcodes for over 400 000 species. Many of these species have been selected because they are of special interest to particular users who need the ability to identify "their" species. However, as a result of our progress more and more we are looking at the completion of larger reference libraries for particular taxonomic groups either world-wide or more limited in range such as national libraries. Building such barcode reference libraries in a systematic fashion can be challenging and comes with its own set of potential issues. 

A new study published in PLoSONE last week uses the work on the DNA Barcode library for the Hemiptera of Canada as an example to look at strategies to construct reference libraries:

We discuss the development of our workflow in the context of prior DNA barcode library construction projects, emphasizing the importance of delineating a set of reference specimens to aid investigations in cases of nomenclatural and DNA barcode discordance. The identification for each specimen in the reference set can be annotated on the Barcode of Life Data System (BOLD), allowing experts to highlight questionable identifications; annotations can be added by any registered user of BOLD, and instructions for this are provided.

The colleagues define reference records as publicly available DNA Barcode sequences linked to voucher specimens via BOLD that:

The resulting library of Canadian Hemiptera covers about 45% of the recognized species (~1850) based on samples of 20,851 specimens belonging to 628 genera and 64 families. The total sampling yielded records for 54,280 specimens, which included 2671 species. These include specimens collected in Canada, in BINs without any named specimens. As such they represent possible new species records on BOLD but they have not been included in the library dataset until further detail becomes available.

As often, the last words of my post belong to the authors of the study:

Lastly, we recognize the multimodal nature of biodiversity inference can be unifying. DNA sequences without names, specimens without sequences, names that are synonymies—can all be reciprocally illuminating in a comparative framework. Conventionally, these frameworks have been important, but isolated works: catalogues, monographs, revisions, descriptions, sequences, and their epistemological foundation—specimens. As demonstrated here, an infrastructure that digitally aggregates specimens in a DNA-mediated reference library can unite these isolated resources into open-sourced ‘virtual unit trays’ of specimens, and sequences, from across the world’s collections. Such an effort integrates isolated resources to create a shared understanding about taxon diversity.

Communicating about how we evolve such an infrastructure is a frontier in biodiversity science. And we share the ideas in this paper to help evolve inference methods that are at once public, repeatable, collaborative, and comparative.