Friday, December 20, 2013

Scandinavian Barcodes

More than a thousand new species –nearly one-quarter of which are new to science – have been discovered in Norway since the Norwegian Taxonomy Initiative began in 2009. This unique effort to find and name all of the country's species  is one of just two government efforts worldwide where research has been funded solely to find and catalog the country's species diversity.

The Norwegian initiative is focused on describing poorly known species groups across the country's varied habitats, which range from alpine plateaus to the arctic. Scientists believe that there are roughly 55 000 species in Norway, but until now only 41 000 of them have been discovered. The 1165 new species discovered by the initiative over the last four years are thus an important addition to this number. Among them are new insect species, lichens, molluscs and cold-water sponges. 

A sub-set of the material collected by the Taxonomy Initiative has been made available for DNA barcoding in collaboration with the Norwegian Barcode of Life network (NorBOL). To date, NorBOL has registered barcodes from approximately 3 800 species in Norway, over half of which have come via the Taxonomy Initiative. This progress likely helped to convince the Research Council of Norway to provide more funding towards national DNA Barcoding. They just announced that NorBOL has been granted about $4.2 to develop the network into a national research infrastructure. 

The project starts in January 2014 and will focus on knowledge transfer and capacity building in all NorBOL member institutions in addition to continue to build a DNA Barcode library for the Norwegian fauna and flora (including fungi). 

Congratulations to the colleagues in Norway - it would be great if other nations would follow this example.

Monday, December 16, 2013

Potato eaters

Flea beetles are small, jumping beetles of the leaf beetle family Chrysomelidae. Many major agricultural crops are attacked by flea beetles. Species of the genus Epitrix, for example, feed mostly on plants from the family Solanaceae (Nightshades) and some of them are major pests of potato crops. What makes pest management so difficult is the fact that Epitrix species are morphologically very similar. Species delineation usually requires dissection and study of genitalia and that in turn requires a high level of expertise (and time, and patience). 

It comes to no surprise that DNA Barcoding is proposed to help with the identification of at least all the economically important Epitrix species especially when considering all their developmental stages at which it is usually impossible to tell what species is which. There are five species of the genus that feed on potato in Europe and North America (Epitrix cucumeris, Epitrix similaris, Epitrix tuberis, Epitrix subcrinita and Epitrix hirtipennis) and they are considered major pests. 

A group of French researchers has tested not only the standard COI barcode region but also ITS2. The latter was used to test for potential ambigous results with the mitochondrial marker. They couldn't detect any mitochondrial introgression. Once the reliability of the DNA Barcode was confirmed the researchers developed an RFLP-based diagnostic method and showed that unambiguous species discrimination can be achieved by using the sole restriction enzyme TaqI on COI polymerase chain reaction products. Now that makes the identification rather simple and considerable cheaper. 

The concluding paragraph of the paper shows how timely this study was:
During the final stages of review of this manuscript, the European commission published a decision (212/270/EU) to prevent the introduction of E. tuberis and E. subcrinita in Europe and limit the spread of E. cucumeris and E. similaris (Official Journal of the European Union, 2012). By enabling the identification of Epitrix specimens at different periods of the life cycle, this diagnostics tool should help member states conducting survey for the presence of potato flea beetles on potato crops as well as other host plant species, as recommended by the European commission. Fast and accurate detection of Epitrix potato flea beetles would help study their potential spread and contribute to their management with minimal disruption to Solanaceae trade.

By they way, BOLD contains quite a few sequences of those species in question some of which actually collected by the School Malaise traps, e.g. this one.

Friday, December 13, 2013

December Bulletin

Another accomplishment of the day:
The new Barcode Bulletin is out! 20 pages that showcase what is currently going on in this field of research, and an Editorial written by yours truly.

A lot of articles represent research and projects that were presented in Kunming. So, this is an excellent opportunity to read over the Holidays what you might have missed because you couldn't attend.

School Malaise Trap Program Fall results

It's time again to share some results of a School Malaise Trap program.Yes, we did it again this fall. From September 23rd to October 4th we had 21 schools catching flying insects with Malaise Traps. All participating teachers will receive an email this afternoon with a big results package.

You might remember that the first run of program involved 60 schools in 42 cities. We had to reduce this for the fall for financial and logistical reasons and we also skipped our usual visit by the BIOBus. Nevertheless, the results were impressive especially given that it was quite late in the season. We were quite curious because by that time of the year we usually remove our traps in the National and Provincial Parks. This would give us an indication what we potentially miss by doing so.

Indeed the trap catches were quite high and despite having only about a third of the spring numbers of traps out, we caught more species. The 21 traps on average collected 1,338 specimens for the collecting period. Our staff sorted 28,110 specimens and selected 5,985 to be barcoded. Our final dataset was made up of 4,736 DNA Barcodes (not all worked and short barcodes were discarded). An impressive number of 1,493 putative species were collected over the two week period of the program. Here a breakdown:

113 of these species were new to BOLD which could either mean that they are known but have not been sampled yet or that they are indeed new to the region or even to science. We also had a look at the amount of overlap between our spring and the fall runs and found out that 404 species occur at both events which leaves us with 2500 species found in two weeks in early spring and two weeks in late fall in 70 schools in south-western Ontario. 

This project is unique in many respects. Firstly, it is a great discovery based science project for classrooms in both elementary and secondary schools. The teacher and student feedback is very positive and the fact that with the help of BOLD we can give credit to each participating group for their contribution to scientific knowledge, is invaluable. Secondly, we have an unprecedented surveillance network in our immediate vicinity. Both runs unveiled a good number of firsts for Ontario, Canada, North America. Just one example encountered last week when looking at the data: The hemipteran Dicyphus errans has only been known from Europe so far where it is used as a biocontrol agent. The new School Malaise Trap dataset contains a record that matches some European counterparts on BOLD. A first quick morphological inspection confirms this. Now a colleague at the CNC (Canadian National Collection of Insects) will look closer and subsequently we will officially report this find. This might be an escaped biocontrol agent used by a local farmer to eradicate aphids. Problem with this species is that once they eat all the aphids or flies they suppose to control they can switch their diet and become a pest themselves.

For the researchers here at BIO the fun starts now. We have so much data to look at and it even if those two events are just taxonomically restricted snap shots they allow us insights into diversity patterns on a scale never possible before. Furthermore, the program has not only excited almost 3000 kids in the region but also considerably helped building our DNA Barcode reference library.

Thursday, December 12, 2013

100 pigeons and their diet

Due to a high degree of faunal and floral endemism oceanic island ecosystems are of high priority when it comes to biodiversity conservation. Evolution under isolated conditions formed unique ecosystems, but those are highly vulnerable to human disturbances, such as deforestation or the introduction of invasive species.

For example knowing the diet of an endangered animal might become very important for adequate restoration efforts on oceanic islands because introduced species may already be a major component of the diets of some endangered species.

The red-headed wood pigeon Columba janthina nitens is a critically endangered subspecies endemic to the Ogasawara Islands, a chain of oceanic islands located 1000 km south of the main islands of Japan. The current population of this species might only comprise of 100 individuals. Furthermore, the native forest of the Ogasawara Islands has been destroyed as a result of human settlements in the 19th century and World War II. As a result the islands are now home to several introduced plants which have expanded their natural range replacing the eradicated local flora. Researchers supected that the red-headed wood pigeon might have shifted its diet in favor of the introduced species in order to cope with the lack of native food resources. 

A group of Japanese colleagues went ahead and tested this assumption by using next-generation sequencing of fecal samples from the birds. They called it DNA Barcoding although they used a different marker (the chloroplast trnL P6 loop) for their analysis. It is not clear why this marker was chosen although it had been used for similar studies before.The disadvantage of using a non-standard becomes clear when reading their publication. In order to get some useful results they first had to construct their own library of reference sequences (over 200 species) before moving on to the fecal samples. Not only does that sound like a lot of extra work but for all other scientists following agreed upon standards this library is not very useful unless they shift their attention to trnL P6. I find this very frustrating as the study as such is great and the results very important for the planning of any restoration efforts:

In this study, a diet analysis using DNA barcoding provided a high-resolution identification of food plants and clearly overcame the bias of traditional microhistological analysis. The results of the DNA barcoding indicated frequent consumption of introduced species, rather than only native species, by the pigeons. The rapid eradication of some introduced species without restoration of the native seed plants may reduce available food resources for this pigeon. Thus, a strategy that balances the eradication of introduced plants and the restoration of native food resources is important. Differences between the composition of pigeon diets on Chichijima and those on Hahajima should also be considered during the restoration of each island. Although some existing technical problems must still be solved (e.g., the discrimination rate of the P6 loop database, sampling strategy), the NGS DNA barcoding approach will provide a better understanding of the food web, including the interactions between native and introduced species and appropriate nature restoration planning for oceanic island ecosystems.

Overall a great example showing the advantages of a deeper understanding of food webs provided through next generation sequencing. If it helps those birds even better. They just shouldn't call it DNA Barcoding because it isn't. 

Tuesday, December 10, 2013

Frosty cockroaches

With winter’s arrival comes the kind of news that may give New Yorkers the creeps. A species of cockroach never found in the United States before has been positively identified in Manhattan and even worse, this variety can survive not just indoors where it’s warm, but also outdoors in freezing temperatures. This species (Periplaneta japonica) is known in Asia, but was never confirmed in the United States.

The Asian species was first spotted in New York in 2012 by an exterminator working on the High Line, an elevated walkway and park on Manhattan’s West Side (see photo). These cockroaches looked different to him, so he sent the carcasses to the University of Florida for analysis. Researchers there used DNA Barcoding to confirm the presence of this new cockroach species. It is not clear how the cockroach arrived in New York City but it is suspected that one or more of the ornamental plants that are planted on the High Line arrived in soil that contained the new pest.

The original paper has been published in the Journal of Economical Entomology but I couldn't find it on their website yet. As soon as I discover a valid link I will share it through the comments.

Friday, December 6, 2013


Like their hymenopteran cousins (ants, bees and wasps) termites (isopterans) live in colonies and divide labor among castes, produce overlapping generations, and take care of their young collectively. A typical colony contains nymphs (half-mature young), workers, soldiers, and reproductive individuals of both sexes, sometimes even several egg-laying queens.There are termite species that do not have a soldier caste at all, and they are fairly well represented in tropical regions of the world, especially South America and Africa. 

Workers take on the defense role by using their gut contents to either seal up nest damage, or trap invading ants which are the predominant invaders. At first glance, it may appear that this defensive method is inadequate, as casualties are often high on the termite’s side, especially in the event that a large breach has occurred and ants manage to invade in large numbers. However, most of these soldierless termite species feed on decaying wood or humus, and thereby largely avoid contact with ants while foraging. 

Species boundaries in termites are traditionally inferred by using morphological characters, although morphology sometimes fails to correctly delineate species. Another commonly used non-morphological taxonomic character is a profile of the cuticular hydrocarbons. They have been proved useful to distinguish a couple of insect species, especially among social insects. Using cuticular hydrocarbon profiles for species recognition is thought to be a direct way to compare the chemical characters through which social insects recognize each other. However, more recently researchers have taken advantage of alternative methods such as DNA Barcoding but nobody really tried using all of those methods simultaneously in an integrative taxonomic approach. 

An international group of researchers has now done this more extensive testing and their paper was published this week:
We sampled soldierless termites in various forest types of the Nouragues Nature Reserve, French Guiana. Our results show that morphological species determination generally matches DNA barcoding, which only suggests the existence of three cryptic species in the 31 morphological species. Among them, Longustitermes manni is the only species whose splitting is corroborated by ecological data, other widely distributed species being supported by DNA Barcoding. On the contrary, although cuticular hydrocarbon profiles provide a certain taxonomic signal, they often suggest inconsistent groupings which are not supported by other methods. Overall, our data support DNA Barcoding and morphology as two efficient methods to distinguish soldierless termite species.

The experienced barcoder is likely not surprised about how well COI sequences work to delineate soldierless termite species. It is remarkable though that cuticular hydrocarbon profiles are not very reliable although they have been portrait as representative for chemical cues the animals actually use to identify members of their own species. Probably there aren't as good as thought.

Wednesday, December 4, 2013

Very old DNA

Sima de los Huesos, the "bone pit," is a cave site in Northern Spain that has yielded the world's largest assembly of Middle Pleistocene hominin fossils, consisting of at least 28 skeletons, which have been excavated and pieced together over the course of more than two decades. The fossils are classified as Homo heidelbergensis but also carry traits typical of Neandertals. Until now it had not been possible to study the DNA of these unique hominins.

A team from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, has developed new techniques for retrieving and sequencing highly degraded ancient DNA. Together with a Spanish team of paleontologists they sampled two grams of bone powder from a hominin thigh bone from the cave. They extracted its DNA and sequenced the mitochondrial genome. By comparing those DNA sequences those of Neandertals, Denisovans, present-day humans, and apes, the researchers calculated that the Sima hominin lived about 400,000 years ago. They also found that Sima hominin shared a common ancestor with the Denisovans, an extinct group from Asia related to the Neandertals, that lived about 700,000 years ago. This find was rather unexpected since skeletal remains carry some Neandertal-derived features.

What I find most intriguing is the simple fact that the colleagues were able to determine an almost complete mitochondrial genome sequence of a 400,000-year-old representative of the genus Homo not buried (and preserved) in Permafrost. I am thinking of all the type specimens we try to obtain DNA Barcodes from. They are much younger but most likely less well preserved. Nevertheless, worth to have a close look at all the methods and tricks used to come up with a mitochondrial genome that old. One thing for sure - they were able to retrieve the full DNA Barcode - just checked it.

Tuesday, December 3, 2013

Tree barcodes

Podocarpaceae is the second largest family of conifers and mainly found in the Southern Hemisphere. The group comprises about 198 species of evergreen trees and shrubs that are sometimes cultivated as ornamentals in suitably warm climates.

It isn't well known and as a result their use is very limited but Podocarpaceae contain a variety of bio–active compounds such as antioxidants, nordi–terpenes, podocarpic acid, and tatarol. Some of these compounds are known to be antimicrobial, fungistatic, or bacteriostatic, others are cytotoxic and could be used in cancer treatment. However, any potential medical use needs further more detailed research. Furthermore, species of Podocarpaceae are of conservation concern primarily as a result of small population sizes and limited available habitat. Twenty–seven Podocarpaceae species are included in the International Union for the Conservation of Nature (IUCN) red list under the categories of vulnerable (10 species), endangered (14 species), and critically endangered (three species). Two species are included in the appendices of the Convention on International Trade in Endangered Species (CITES): Podocarpus parlatorei is listed in Appendix I (trade is not allowed) and Podocarpus neriifolius is listed in Appendix III (trade with, some limitations, is allowed). That and a slow rate of growth for most species makes harvest of Podocarpaceae generally unsustainable and would require extensive conservation management efforts.

In addition accurate identification of tropical forest trees, such as Podocarpaceae, is often very difficult. The most easily accessed material is usually sterile. If fertile material is present, it is frequently either inaccessible or detached from the tree making it difficult to convincingly associate the fertile and sterile portions. Although sterile material of Podocarpaceae can usually be identified to genus using phyllotaxis and leaf form, accurate species identification often requires careful microscopic examination of internal and external characteristics. Proper use of the existing identification tools requires training in botanical terminology, skill in microtechnique, and familiarity with Podocarpaceae.

Now a team of US and German researchers build a DNA Barcode library for 145 of the species (73% of the family). They generated matK, rbcL, and nrITS2 sequences. In addition, they created a living Podocarpaceae collection in the Botanic Garden of the Ruhr-Universität in Bochum, Germany which promotes the protection of rare and endangered species. There the species will be propagated and passed on to other botanic gardens worldwide.

The discrimination power of matK, rbcL, and nrITS2, individually and in combination was relatively low (56.7%) in this study. The authors also state that this is not unusal and that plant DNA Barcoding studies that heavily sample within taxonomic groups usually report low rates of species discrimination. They suggest that sequences of some unlinked genetic markers may however increase the rate of species discrimination. 

Monday, December 2, 2013

An overlooked giant

Giant clams are among the most conspicuous marine invertebrates on coral reefs due to their large size. Some species can grow up to 230 kg. Species of the genus Tridacna also show a brilliantly colored mantle that contains photosynthesizing symbionts (dinoflagellates of the genus Symbiodinium).

Many of those clams have been harvested for their meat and their shells They are also in demand on the ornamental aquarium market. All that led to widely depleted stocks. Consequently, most Tridacna species are listed by CITES and the IUCN Redlist. A crucial part of conservation management of those giant clams is the proper identification of different species and an estimation of the size of their breeding populations. Many of them are so called broadcast spawners which means eggs and sperm meet freely in the water column. This in turn means that a critical mass of individuals in an area is needed to ensure that eggs and sperm are likely to meet.

A new species of giant clam, thought to have been another well-known species (Tridacna maxima), has now been discovered on reefs at Ningaloo in Western Australia and the Solomon Islands. Individuals looked almost identical to the common species Tridacna maxima, but were actually genetically quite different. The Australian researchers used DNA Barcodes and other DNA regions to study gene flow of different Tridacna species and came across this cryptic species by chance.

This could turn out to be a very important discovery as chances are high that scientists have been overestimating the population of related species of clams. If this new species was mistaken and counted for Tridacna maxima the population size of that species would likely be estimated to be larger than it actually is. Given the conservation status of these majestic animals this is potentially bad news as population estimates need to be adjusted downwards.

Thursday, November 28, 2013

Microbial vintage

It always has been a very important questions to some - What makes a great wine? Answers to this question have been - to say the least - diverse: the right soil, a good grape, a competent winegrower, etc. Well, it looks like we have to add one more item to the list - good bacteria.

On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone.

Researchers from the University of California, Davis, analyzed grape samples from eight California wineries and found that microbes factor into the way wines taste from region to region. In total they collected 273 grape must samples. Must is actually a term for wine grapes that have been plucked from the stem and crushed together. The reason why the researchers decided to use must, and not just individual grapes, was because individual grapes - even from the same vineyard - can have different microbial communities on them. Using must was a rather simple way of pooling the samples.

The study used a high-throughput, short-amplicon sequencing approach (Illumina platform) with primers for the V4 domain of bacterial 16S rRNA and the internal transcribed spacer (ITS) DNA Barcode to identify the types of bacterial and fungal species in each set of must. 

They found that different bacterial compositions were present in different regions, potentially giving grapes a distinctive taste or in the worst case - ruining them. Lactic acid bacteria, for instance, were found to be common in the Napa Valley. Lactic acid bacteria can lead to the spoiling of wine, but they are also capable to turn malic acid into lactic acid, which gives a Zinfandel wine a distinct taste. Species composition differences between regions might also contribute to differences of taste between two Zinfandel wines.    

This metabarcoding approach makes it possible to ascertain which specific microbes and combinations of microbes are more or less important for the quality of a given wine in a given vineyard over time. The consistency of the microbial diversity over time may ultimately contribute to the quality of a wine and the reputation of vineyards. However, whether these regionally different microbiota actually directly modulate wine sensory qualities must be experimentally tested, as do pretty much all putative features of wine terroir.

We demonstrate that grape-associated microbial biogeography is nonrandomly associated with regional, varietal, and climatic factors across multiscale viticultural zones. This poses a paradigm shift in our understanding of food and agricultural systems beyond grape and wine production, wherein patterning of whole microbial communities associated with agricultural products may associate with downstream quality characteristics. Elucidating the relationship between production region, climate, and microbial patterns may enhance biological control within these systems, improving the supply, consumer acceptance, and economic value of important agricultural commodities.

Tuesday, November 26, 2013

Dog parasites

The Chinese province of Qinghai on the Qinghai-Tibetan Plateau is one of the most highly endemic areas for Echinococcus parasites. Nomadism of high-altitude adaptive animals,  such as yak and sheep, is very popular, and most farmers keep dogs for protection and for herding.  Together, these conditions favor both endemism and the lifecycle of taeniid cestodes. Dogs are also infected with parasites by eating rodents in the pasture. The prevalence of Echinococcus in humans was determined at 6.1% for Echinococcus granulosus and 5.1% for Echinococcus multilocularis in the Qinghai Province. The prevalence in domestic animals was very high with the reported values reaching over 50 % for Echinococcus granulosus in dogs, yaks and sheep. Dogs also serve as the definitive host for Taenia species which also can infect other domestic animals, such as yaks and sheep, and thus would reduce animal health and affect meat quality. The life cycle of the parasites connects both dogs and livestock (see figure above). 

A variety of methods have been used to diagnose taeniid infection in dogs. One common method for diagnosis in live dogs is the examination of fecal eggs. While this has been difficult in the past as eggs don't show a lot of species specific features DNA Barcoding is used in more recent studies. For a new study, researchers collected dog feces before and after deworming at a pilot site in the Qinghai Province and thereby determined an optimal sampling schedule for egg examination. By using this method, they were able to evaluate the prevalence of taeniid cestodes in dogs at different sites in the Province. Subsequently one site was selected and the team conducted a control trial of taeniid infection in dogs with periodic deworming treatment. 

Analysis of 277 dog feces revealed that taeniid cestodes, including Taenia species and Echinococcus granulosus, were e.g. highly prevalent in one region (34.4%), but no eggs were found in a region where a control trial on canine echinococcosis had been conducted 20 years ago. The first region was chosen for the control trial with the result that he prevalence of taeniid cestodes in the dogs was reduced to 9.6% and 4.9% after one and two years, respectively,  indicating that some dogs did not receive proper treatment. The researchers went back and conducted a survey among the farmers which revealed that most farmers were not familiar with echinococcosis or the transmission route of the disease. All these findings imply that DNA Barcoding utilized for species identification and a program for educating local farmers will greatly improve infection control.

Monday, November 25, 2013

Black flies

Black flies are members of the fly family Simuliidae. To date over 1,800 species of black flies are known. Most species belong to the large genus Simulium. Most black flies feed on the blood of mammals, including humans, although the males feed mainly on nectar. The ones feeding on human blood are a nuisance as the insects use their very short mouthparts that are sharp enough to cut into the flesh of their victim and lick the blood that comes out. A blood meal lasts about 3-6 minutes and can even go to 15 minutes. During this meal, a female eats as much blood as its own weight. In order to make the process more effective the insect injects saliva and an anticoagulant. The latter causes swelling and itching, and I can attest that the latter is really a nuisance. Also unlike the mosquito, black flies attack in silence without a distinct buzz.
Black flies are small insects, black or gray, with short legs, and antennae. They are known to spread several diseases, including river blindness in Africa and the (Central and South ) Americas.

Black flies are a nightmare for traditional taxonomy because of their small size and structural homogeneity. Banding patterns of the polytene chromosomes (cytotypes) have been the standard in addressing this challenge, but require experienced people to interpret them and typically are workable only for certain larva stages. 

Two researchers have now examined the efficiency of DNA Barcoding for differentiating morphospecies and cytoforms of species complexes occurring in Thailand:

A total of 351 cytochrome c oxidase subunit 1 sequences were obtained from 41 species in six subgenera of the genus Simulium in Thailand. Despite high intraspecific genetic divergence (mean = 2.00%, maximum = 9.27%), DNA barcodes provided 96% correct identification. Barcodes also differentiated cytoforms of selected species complexes, albeit with varying levels of success. Perfect differentiation was achieved for two cytoforms of Simulium feuerborni, and 91% correct identification was obtained for the Simulium angulistylum complex. Low success (33%), however, was obtained for the Simulium siamense complex. The differential efficiency of DNA barcodes to discriminate cytoforms was attributed to different levels of genetic structure and demographic histories of the taxa. DNA barcode trees were largely congruent with phylogenies based on previous molecular, chromosomal and morphological analyses, but revealed inconsistencies that will require further evaluation.

Friday, November 22, 2013

BIO image of the day

Our BIO image of the day got even better. By using some new mapping tools on Pinterest specimens presented come with more geographical information. For everyone interested in more detail there are always links to the specimen on BOLD and to its BIN page. 

Wednesday, November 20, 2013

Farewell Frederick Sanger

Frederick Sanger passed away yesterday at the age of 95.

Especially as DNA barcoders we have to give kudos to him as he was the pioneer that developed DNA sequencing, and most of the time we refer to the classical chain-termination method of DNA sequencing as Sanger-sequencing.

His group was actually the first that produced a whole genome sequence, made up of more than 5,000 basepairs, in a virus. Sanger was the only scientist to have been awarded the Nobel prize for Chemistry twice. The first one he received in 1958 for developing techniques to work out the precise chemical structure of proteins especially the one for insulin. The second prize he received together with Walter Gilbert and Paul Berg in 1980 for developing the chain-termination method to determine the nucleotide sequence of DNA. This invention represents the beginning of modern genetics with all the genome sequencing projects and - DNA Barcoding which despite newly developed sequencing technologies still is the method of choice for any sequence library building effort, e.g. all of 2.6 Million barcode sequences on BOLD are the result of Sanger sequencing.

A great scientist left us yesterday and one of his many qualities was modesty:

I was just a chap who messed about in his lab.

Friday, November 15, 2013

Effective Biodiversity Conservation

Although protected areas (PAs) cover 13% of Earth's land, substantial gaps remain in their coverage of global biodiversity. Thus, there has been emphasis on strategic expansion of the global PA network. However, because PAs are often understaffed, underfunded, and beleaguered in the face of external threats, efforts to expand PA coverage should be complemented by appropriate management of existing PAs. Previous calls for enhancing PA management have focused on improving operational effectiveness of each PA [e.g., staffing and budgets]. Little guidance has been offered on how to improve collective effectiveness for meeting global biodiversity conservation goals. We provide guidance for strategically allocating management efforts among and within existing PAs to strengthen their collective contribution toward preventing global species extinctions.

This is the first paragraph of a new study just published in Science in which colleagues identified the protected areas most critical to preventing extinctions of the world's mammals, birds and amphibians. Resulting from an international collaboration, this analysis provides practical advice for improving the effectiveness of protected areas in conserving global biodiversity.

The researchers calculated what they called 'irreplaceability' of individual protected areas, based on data on some 173,000 terrestrial protected areas and assessments of 21,500 species on the IUCN Red List. Their analysis looks at the contribution each protected area makes to the long-term survival of species.
Figure taken from Le Saout et. al. 2013

As a result, 78 sites have been identified as exceptionally irreplaceable. Together, they harbor the majority of the populations of more than 600 birds, amphibians, and mammals, half of which are considered globally threatened. In many cases these areas protect species that cannot be found anywhere else. Many are already designated as being of 'Outstanding Universal Value' under the UNESCO World Heritage Convention. These sites include the Galápagos Islands, the Manú National Park in Peru, and the Western Ghats in India. However, half of the land covered by these areas does not have World Heritage recognition. This includes for example the Udzungwa Mountains National Park in Tanzania, the Ciénaga de Zapata Wetland of International Importance in Cuba, and -- the most irreplaceable site in the world for threatened species -- the Sierra Nevada de Santa Marta Natural National Park in Colombia.

One needs to keep in mind that such a study can only be the beginning. All analyses focused on three groups representing the world's terrestrial vertebrate diversity. The advantage is the amount of data available for those animals but there is also a very practical reason to look at them first:

Local management plans often focus on charismatic species, and management decisions favoring these (e.g., habitat protection) will often benefit a whole set of species. However, management objectives established for particular species sometimes deliver no benefits to, or can even jeopardize the persistence of, other species. In such cases, we propose that species for which a PA has the highest conservation responsibility should be the first consideration for management and monitoring.

I guess we should be thinking of doing similar assessments for marine areas and of course for all other life on earth as: 

PAs are our main hope for meeting ambitious global conservation targets, such as preventing species extinctions, but the costs of ensuring their effective management are substantial, albeit affordable. We hope that the conceptual guidance and specific data provided here will support strategic reinforcement of the world's existing PAs, to improve their individual and collective effectiveness for conserving global biodiversity.

Thursday, November 14, 2013

Gleanings from the Kunming conference - Underground trees

In South Africa's coastal grasslands, you can explore a forest by literally walking along its canopy. It is home to some extraordinary tree species which are called underground trees. Only the uppermost leaves and branches of the tree are visible. The rest of the tree is submerged below the deep sandy soil, creating a clonal network of underground forests.

Prof. Braam van Wyk, plant taxonomist from the University of Pretoria explains those specialized plants (the correct scientific term is pyrogenic geoxylic suffrutices):
It is a very peculiar growth form that is associated with our grasslands, and it is very much a type of growth form in Africa. It is not found in significant numbers anywhere else in the world, except perhaps to a limited degree in South America. It is a growth form where you get plants, woody plants that can be compared to underground trees, and all that you see are these green twigs which can be compared with a canopy of the tree. And this is probably one plant sitting here, or maybe even this whole area may be one plant, and it’s the canopy that just sticks out, the tips of the branches above ground. These tips may burn down every year, but the rest of the tree stays untouched underground. Why they have adopted this strategy… it is a very interesting challenge to come up with reasons. Fire, frost, a shallow water table and grazing have all been considered. There are lots of interesting things we can say about the reasons why plants have adopted this strategy and why it mainly evolved in Africa. They are called clones, and are essentially immortal, nothing can kill them, except for habitat destruction. Grazers can not kill them, fire can not kill them and they are drought resistant. They grow extremely slowly, and if you look at the diameter of some of these clones, they must be the oldest inhabitants of our grasslands. I would say easily more than a thousand years for many of these clones since the first seed arrived for that particular species. But I would not be surprised if some of them are one day shown to be perhaps more than 10 000 years old, amongst the oldest plants in the world, much older than any tree that you are going to see. They are very peculiar plants and we have quite a number of these species in our grasslands.

It was during Michelle Van der Bank's (University of Johannesburg) talk at the conference in Kunming that I first learned about these extraordinary trees. Michele was reporting on results of the TreeBOL Africa project. They have cataloged and barcoded over 50% of the estimated 2,486 woody shrub and tree species in southern Africa. The underground tree species were one example of how this dataset was used to address questions across disciplines including ecology, conservation biology, and taxonomy.

Wednesday, November 13, 2013

Gleanings from the Kunming conference - frosty springtails

Ask anyone to name an Antarctic land animal, the response most likely will be, "penguin." However, most of the usual suspects — penguins, seals — don't actually live on the continent. They just visit. With the exception of the emperor penguin all species spend most of their lives at sea. Actually, in order to see Antarctica's resident land animals, you have to look through a microscope. The animals that rule Antarctica are rotifers, tardigrades, mites, and springtails possessing a bizarre array of physiological tools and strategies to survive on the coldest, windiest, highest and driest continent on Earth.

Springtails for example are found all over the planet, but those that live in Antarctica have a few tricks to survive the harsh conditions. They can slow down their metabolism to save energy, and shortly before winter, they start to produce glycerol - the very same substance we use in our cars to prevent cooling water from freezing.

Ian Hogg and his team at the University of Waikato have been studying springtails in Antarctica for quite some time and some of their research was presented in Kunming.

They used DNA Barcodes to examine levels of genetic variability within and among populations of five endemic springtail species along a latitudinal gradient in the Ross Sea region of Antarctica. This work represents the first re-evaluation of several areas, including the central and southern Transantarctic Mountains, in almost 50 years. Three of the five species showed high levels of divergence at both small (<15km) and large (>300km) spatial scales. For example, Gomphiocephalus hodgsoni, a widespread and common species showed 7.6% sequence divergence on opposite sides of the Mackay Glacier and >8% when compared with sites near another glacier. The other two species (Neocryptopygus nivicolus and Antarctophorus subpolaris) also showed high levels of sequence divergences despite being more range-restricted. 

What are the potential reasons for such high barcode divergences? The colleagues conclude in their abstract:
... glaciation in Antarctica has promoted and maintained the levels of diversity observed among populations of springtails and that isolation has occurred even on relatively small spatial scales. Levels of divergence are likely to reflect the presence of previously unknown or cryptic species and conservation efforts should be directed towards protecting and preserving the biotic integrity of fragmented landscapes in Antarctica.

Tuesday, November 12, 2013

Gleanings from the Kunming conference - ECO-TROP

I've promised some posts about what I learned in Kunming during the International Barcode of Life Conference. Lot's of exciting new research ideas, interesting projects and astonishing results.

Let's start with a field school that integrates DNA Barcoding into an educational program that develops a census of invertebrate diversity in a National Park in Gabon.

Gabon is considered one of the world's major biodiversity hotspots. The forests and savannas covering most of the country are popular for their enigmatic species of vertebrates and higher plants. However, as usual, 
invertebrates are poorly known and as a consequence generally absent from conservation plans and strategies. DNA Barcoding seems to be the ideal tool to help with documenting basic descriptive metrics of invertebrate diversity (e.g. species richness, spatial or temporal turnover). 

Back in 2011, the first edition of the “field school in tropical ecology and palaeoecology” (ECO-TROP) was organized  in the National Park La Lopé (Ogoué Ivindo region) with the participation of several institutions from France*

The organizers think that DNA Barcoding is an unique educational tool to raise students’ awareness that can also assist and hopefully promote the future census and description of the local diversity. DNA Barcoding represents a central theme of this successful training program, strongly emphasizing its potential for the documentation of biodiversity in poorly known and hyperdiverse groups of invertebrates. 

Undergraduate students students from universities in France and Gabon are introduced to common invertebrate sampling methods which are routinely used in studies on biodiversity, ecology and palaeoecology in intertropical environments. The field course takes into account the lack of taxonomic information for these organisms and illustrates – both in the field, during short seminars and lab work sessions – the strength of an integrative approach to taxonomy (morphology and DNA), but also the value of a multidisciplinary approach by integrating ecological observations and measurements (e.g. soil profiles, vegetation structure), geographical factors at various scales (through aerial and satellite image analyses). Students also learn about the influence of past human occupation in these areas and their impact on the environment.

The ECO-TROP field school runs annually, with the prospect of moving to other National Parks of the country. The expectation is that all editions of ECO-TROP will significantly contribute to the knowledge of Gabon’s invertebrate biodiversity and, more importantly, to equip young field biologists with a solid understanding of ecological and conservational issues in relation to biological diversity, and in particular on the importance of invertebrates in ecosystems. 

h/t Thibaud Decaens

*Université de Rouen, Institut pour la Recherche et le Développement (IRD), Université de Rennes, Centre National de la Recherche Scientifique (CNRS) – and Gabon – Agence Nationale de Parc Nationaux (ANPN), Université de Masuku (USTM), World Conservation Society (WCS), Complexe Educatif Docteur Alphonse Mackanga Missandzou (CEDAMM), Institut de Recherche en Agronomie Forestière (CENAREST–IRAF)

Monday, November 11, 2013


The hemipteran Phylloxera (Daktulosphaira vitifoliae) is a pest of commercial grapevines worldwide, originally native to eastern North America. These tiny insects, related to aphids, feed on the roots and leaves of grapevines which results in root deformations and secondary fungal infections. Juveniles also form protective galls on the undersides of grapevine leaves of some vine species.

The species has already spread and is found around most of the world's vineyards. One of Australia's primer vine regions - South Australia is home to the Phylloxera and Grape Industry Board of South Australia which is committed to minimising the risk of pests and diseases in particular Phylloxera in South Australian vineyards. The organisation has been spearheading research that resulted in the development of DNA tests (DNA Barcoding, eDNA analysis with taqMan probes). In order to support these efforts the South Australian Government has decided to spend $500,000 to speed up commercialisation of this new method of testing for phylloxera.

Traditional testing methods rely on digging around grapevines followed by visual inspection to see if the insect is living on the roots. If done comprehensively this method is extremely costly and the new DNA-based analysis could save the industry millions of dollars. Trials were already conducted in New South Wales and France and researchers are now looking into refinement of sampling protocol the need to establish the best location and depth to take a sample from, and how long it will take and at what temperatures before the DNA degrades’.

Save the vine!

Thursday, November 7, 2013

The cave cyber-centipede

A description of a new centipede species went through the press last week. Not so much because of the fact that it represents a very exotic find or bears a particular interesting name but rather because of the amount of additional information provided in addition to the usual data:

We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae),  found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour....

...This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.

Well, this is certainly not meant as a contribution to more faster descriptions (turbo-taxonomy). The international team of researchers sees it rather as a way to describe species in the future with as much information as possible. It also represents a rare type of collaboration between scientists, publishers (GigaScience, Pensoft) and genomic institutions (China National GeneBank, BGI-Shenzhen). 

Frankly, I am not sure what to make of this project. More data sounds great and more comprehensive descriptions of organisms are certainly very attractive. However, I strongly believe we do need to focus more on changing our ways to register and describe species as we seriously fall behind in our efforts to catalog biodiversity before it is wiped out by humanity. For this reason I do think the conclusion of the publication is perhaps a bit too enthusiastic although the point they make about standardization is one I do support:

Taxonomy is at a turning point in its history. New technologies allow for creation of new types of information at high speed and in gigantic volumes, but without clear rules for communication standards, we will not be able to exploit their full potential. We need to focus our efforts on linking these bits and pieces together, by documenting them, by standardising them and by making them retrievable. If such an infrastructure is in place, unforeseen analytical powers can be unleashed upon these data, creating a revolution in our abilities to understand and model the biosphere.

Wednesday, November 6, 2013

BIO's Daily Image

I am slowly catching up on my email and marking of course assignments. There is a lot left to report on the Kunming conference. Unfortunately, the connection at the site was not good enough (let alone the problem of blocked sites such as blogger) to provide proper updates. I will make up for that in the days to come.

Another thing that perhaps went largely unnoticed is a new feature we started about a week ago:
BIO's Daily Image
Our collections unit is also responsible for proper imaging of all specimens that go through our pipeline. Any specimen that arrives here will be photographed before tissue samples are taken and passed on to the lab for sequencing. As you can imagine over the years we have been amassing quite a few images of beautiful critters and every day we keep adding new ones. All of the images are uploaded to BOLD together with all other data associated with a specimen but we thought it would be a great idea to share some of them through another outlet on a daily basis. We chose Pinterest for that as it is most convenient and up-to-date. Furthermore, we can use widgets for our websites. I've added one to this blog (you should be able to see it in the column on the right). Enjoy!

Thursday, October 31, 2013

The Kunming declaration

Today the Kunming declaration was officially announced. Essentially it represents the starting point for a professional society for DNA Barcoding. On Monday participants of the conference had a chance to share ideas with respect to a society and its potential role. Throughout the week a small group formulated a document that was officially read and signed at tonight's conference gala.

Here's the document:

Conference - Day 2

Day 2 at the International Conference for the Barcode of Life was a rather short one as the afternoon was free giving the participants a chance to explore the world outside the hotel and conference venue. A small group of us traveled to the so called Stone Forest which is worth another post I'll put up once I am back and had a chance to download my photos.

What was there to learn?
The plenaries of this day were under the title Implications for Biodiversity. A diverse set of talks which makes it hard to for me to summarize so I will just throw out some citations and ideas that I put down during the session. Of course they are taken out of context but I think they speak for themselves:

"Coldcode members are proud to say that we are a-political"
Bob Murphy (a Chinadian)

"A future research agenda for DNA Barcoding:
1.describe biodiversity patterns from site-base DNA sequencing (genomic observatories), long term ecosystem monitoring using barcodes
2.assess lineage specific and area specific rates of turnover for each ecoregion in the world"
Alfried Vogler

"We need no more keys. They are a waste of time"
Michael Balke

"Ultra-deep sequencing leads to ultra-deep frustration in protists with sometimes >80% unassigned OTUs"
Jan Pawlowski

"Mushroom poisoning is a big issue in China and DNA Barcoding can make a big contribution to local markets and save lives."
Zhu-Liang Yang

"Scientific naivety is unwarranted"
Gary Saunders

Needless to say that I want to make sure that everybody learns more about the talks than a few text bits that I picked entirely subjectively some of which because I thought they are very entertaining. If you want to read more you will have to follow this blog for the next couple of weeks.

Tuesday, October 29, 2013

Conference Impressions - Day 1

The International conference in Kunming is already running in full swing and I found a way to provide some posts while I am still here. Needless to say my posts can cover only a fraction of what was going on in all the sessions and I am not able to attend at all of them. However, I will follow up on some interesting stories and post them after the conference is over.

Here are four of my highlights of the day:

Paul Hebert shared his vision of a BIN registry as an amendment to the current binominal naming system. This is not intended to replace the current taxonomic naming system but to add a structure that helps dealing with the rapidly growing number of species that are waiting for a formal description. He compared this to other systems such as the registry of chemical compounds and the registry of stars and galaxies. In both cases the scientific communities historically had been using conventional naming systems for a long while before they realised that the amount of potential records exceeds human capabilities to name them all in a reasonable time span.

Plant markers
It is remarkable that the plant community represents the largest group at this conference and consequently we have six parallel sessions for plant related topics. During Pete Hollingsworth's plenary contribution it became clear once more that the quest for additional markers is not over. The two current standards rbcL and matK represent a good proxy and work in a considerable amount of cases quite well. No surprise as this is why they were chosen. However, since the Adelaide conference it is known that at least one more is needed to cover some groups. Some people proposed ITS as one option already a few years ago but this idea was met with a lot of scepticism and nobody thought it makes sense to invest in further research. Not the botanists here at the Kunming Institute of Botany, CAS. They actually did a large scale test which clearly showed the advantages of ITS and at this conference some of the initial sceptics actually admitted that this research is indeed very convincing. Certainly a nice Chinese success story which already came out at the end of 2011 but it took a while to gain further acceptance in the community.

In a number of talks and discussions participants stressed the importance of using BOLD as repository for barcodes and workbench. Gerhard Haszprunar from the Zoological States Collections in Munich reported that one reason for the success of Barcoding Fauna Bavarica was the consequent use of BOLD for project and data management. This also saved a considerable amount of costs which made the project more attractive for funders.

Kunming declaration
The day ended with a general discussion about the foundation of a society for DNA barcoding. The goal is to end the conference with a declaration that sets the stage for such a association. Of course there were a multitude of ideas what the roles of such a society should be but the community overall agreed that there is a real need for it. One of the visions for the future of DNA barcoding is that it should play a central role in conservation efforts to protect the world's biodiversity. The conference chair De-Zhu Li stressed this several times throughout the day and stated that he sees it at the centre of future activities as it has the potential to create real diversity baselines and meaningful monitoring programs.

Thursday, October 24, 2013

New Bulletin

In time for the upcoming conference in Kunming we finished another issue of the the Barcode Bulletin. A mix of information on the conference and articles on DNA Barcoding research and applications.

Enjoy reading this for a while. This will be the last post for the coming days. I will be at the International Conference in Kunming but unfortunately it looks like I won't be able to use Blogger in China. So, please be patient - all the news will be posted upon my return.

Tuesday, October 22, 2013

Itsy-bitsy spider

The Entomological Society of Ontario and the Entomological Society of Canada are currently having their Joint Annual Meeting here at the university and this afternoon we will have some organised tours at our institute. I thought this post might be a good fit :-)

Initially I found it hard to believe but some entomologists despite choosing a career working with insects, exhibit negative feelings toward spiders which range from mild disgust to extreme arachnophobia.

A new paper in the journal American Entomologist features the results of a survey involving a number of arachnophobic entomologists (41) who were asked questions about their fear of spiders. Although most of them only showed mild disgust or mild fear, they still claimed to react differently to spiders than to insects. Other respondents clearly scored in the clinically arachnophobic range and react strongly to spiders.

Some of the entomologists developed their negative feelings toward spiders in childhood and these feelings were not overcome in adulthood. In general the study shows that entomologists have a lot in common with arachnophobes in the general public despite the great morphological diversity that insects exhibit and despite years of professional exposure to insects.

Despite the assumption that entomologists would extend warm feelings toward spiders because of their habituation to arthropods in general, arachnophobia does occur in some members of our profession. For these people, two more legs makes a big difference.

Friday, October 18, 2013

DNA Fingerprinting of Pearls

Pearls produced by oysters of the Pteriidae family are among the most valuable and oldest gems. Oyster shells and pearls have been used for human adornment since antiquity. Today pearls are cultured in domesticated saltwater oysters and freshwater mussels and have become a billion dollar industry. Whereas a natural pearl forms without any human intervention in a wild oyster, a cultured pearl is the result of a human-induced injury. The value assigned to a pearl depends largely on its quality, rarity, and whether it originated naturally or through culture. Thus there is significant interest in being able to scientifically document the provenance of both historic natural pearls and modern cultured pearls. This is rarely possible for the most valuable white to slightly cream-colored pearls using current methods such as UV-visible photospectrometry and micro-Raman spectroscopy. The higher value of natural pearls has led to many fraudulent attempts to pass off cultured pearls as natural ones. To date, the distinction between natural and cultured pearls has been based on X-ray shadow images and more recently X-ray computer microtomography.

Now a group of Swiss researchers successfully developed a DNA-based method to determine the oyster species that produced a pearl as a first step towards providing more precise information regarding its likely geographical origin. Their DNA fingerprinting technique can be used to differentiate pearls from different oysters that were deliberately or accidentally mixed and may eventually differentiate cultured pearls that have been mixed in with natural pearls.

Although largely build from calcium carbonate pearls contain up to 4% organic matter which seems to contain enough well preserved DNA even when pearls were harvested years earlier. The research group was able to recover sequences from different loci (ITS, 16S, COI) longer than 650bp. For better success the team had also developed a micro-drilling technique to extract the DNA. This drilling does not affect the commercial value of an investigated pearl.

h/t Claudia Steinke

BIO Video

One of my jobs here is outreach and that part kept me a little busy over the last weeks. Together with a local production company we made a promotional video for the Biodiversity Institute of Ontario. We're quite pleased with the outcome:

Wednesday, October 16, 2013

Herbal products

Most of the herbal products tested were of poor quality, including considerable product substitution, contamination and use of fillers. These activities dilute the effectiveness of otherwise useful remedies, lowering the perceived value of all related products because of a lack of consumer confidence in them. We suggest that the herbal industry should embrace DNA Barcoding for authenticating herbal products through testing of raw materials used in manufacturing products. The use of a standard reference material DNA herbal barcode library for testing bulk materials could provide a method for 'best practices' in the manufacturing of herbal products. This would provide consumers with safe, high quality herbal products.

That's from the abstract of a new publication that caused a bit of a hype in the press during the last few days. Colleagues here at the institute tested a variety of herbal products using DNA Barcoding. They published their finding in BMC Medicine and given their results it is no wonder that it got picked up by the press

We recovered DNA barcodes from most herbal products (91%) and all leaf samples (100%), with 95% species resolution using a tiered approach (rbcL + ITS2). Most (59%) of the products tested contained DNA barcodes from plant species not listed on the labels. Although we were able to authenticate almost half (48%) of the products, one-third of these also contained contaminants and or fillers not listed on the label. Product substitution occurred in 30/44 of the products tested and only 2/12 companies had products without any substitution, contamination or fillers. Some of the contaminants we found pose serious health risks to consumers.

So, not only 'just' substitution and mis-labelling but also serious health risks through fillers and contaminants. One product labeled as St. John's wort (Hypericum perforatum) was actually fully substituted with Senna alexandrina which can cause adverse effects such as chronic diarrhea, cathartic colon, liver damage, abdominal pain, epidermal breakdown and blistering.

A Ginkgo product was contaminated with black walnut (Juglans nigra). If those traces were from the nuts this could lead to some severe problems for people with nut allergies. However, even if you are not allergic to nuts there is a problem as walnut leaves, woods, bark and fruits all contain juglone which has been listed as tumor agent that is known to promote skin tumors.

A while ago I wrote about a similar study that was done on a much smaller scale to serve as prove of concept. Seems there is a lot more going on in this industry than we initially thought and it would send a strong positive signal out to consumers if science, industry, and regulatory institutions could jointly work on fighting the unethical activities of some manufacturers. Again, no excuse - the tools are in place and we are working on the reference libraries to make them most efficient.