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.

Tuesday, October 15, 2013

Grass miner moths

Rapid development of broad regional and international DNA barcode libraries have brought new insights into the species diversity of many areas and groups. Many new species, even within well-investigated species groups, have been discovered based initially on differences in DNA barcodes. We barcoded 437 collection specimens belonging to 40 pre-identified Palearctic species of the Elachista bifasciella group of moths (Lepidoptera, Elachistidae). Although the study group has been a subject of several careful morphological taxonomic examinations, an unexpectedly high number of previously undetected putative species is revealed, resulting in a 34% rise in species number in the study area. The validity of putative new species was subsequently supported with diagnostic morphological traits. We show that DNA barcodes provide a powerful method of detecting potential new species even in taxonomic groups and geographic areas that have previously been under considerable morphological taxonomic scrutiny.

This abstract is from a new study by Finnish researchers recently published in Nature Scientific Reports. They targeted Palearctic members of Elachista bifasciella group. The moth genus Elachista comprises some 700 species in total, 130 of which belong to the group studied. All have one thing in common - they are difficult to identify as they are small, uniformly colored, with only minute morphological differences. However, they have been subjected to thorough morphology-based taxonomic investigations during the past decades covering the fauna of the entire Palearctic region.

Given the small amount of differences between the species in this group it had been assumed that species have diverged rather recently. This would in turn mean that DNA Barcoding runs the risk of not working properly due to issues such as incomplete lineage sorting or mitochondrial introgression. Well, that does not seem to be the case in this study:

The original analysis of data revealed several species having considerable (>1%) intraspecific variation and likewise clusters of unidentified specimens showing a distinct gap (>1%) from any pre-identified specimens. Altogether, twenty-five such cases were detected. All these were subjected to an in-depth morphological examination. This resulted in the detection of sixteen putative new species whose species integrity was independently supported by genetic and morphological uniqueness.

Even after some years in the business it is always surprising to see how well the method actually works. Even if we have initial reservations.

In summary, our results support many earlier observations that DNA barcodes effectively differentiate closely related species. We demonstrate that a comprehensive sampling of collection material is an efficient way to discover hidden portions of biodiversity and that by accelerating taxonomic workflow DNA barcoding provides an important tool that, when widely used, might substantially help to overcome the taxonomic impediment. Lepidoptera represents one of the most thoroughly investigated groups of insects, and our focal group has been under considerable previous taxonomic investigation. Our results therefore suggest that the assessment of insect species number may often be underestimated by the overlooking of morphologically similar species. Along with growing DNA barcoding activity, we assume an increasing rate of discoveries of new species across all insect groups and areas.

Barcoding Life Highlights 2013

The Fifth International Barcode of Life Conference is quickly approaching. In advance of the conference in Kunming, I've received the Barcoding Life Highlights 2013. This illustrated report focuses on highlights since the Fourth International Barcode of  Life Conference in Adelaide, 2011. It was designed and written by my barcoding blog colleague Mark Stoeckle with assistance from Paul Waggoner and Jesse Ausubel.

Eight pages packed with information including an extensive list of links to websites that are related to DNA Barcoding. 

Have a look!

Wednesday, October 9, 2013

Barcoding Fauna Bavarica 2

It seems to be a great week for German DNA Barcoding. After posting on the announcement of an award to the Zoological Museum Alexander Koenig in Bonn I received news that the prestigious project "Barcoding Fauna Bavarica" will receive another Euro 750 000 from the Bavarian State Ministry for Science, Research and the Arts for five more years work on the project. 

The project aims to barcode the entire fauna (and subsequently other life as well) of the German state Bavaria. Bavaria is home to about 34 000 animals species and in the last four years the project managed to barcode over 11 000 of them. Here is a video that nicely summarizes the campaign:

The project is run by the Bavarian State Collection of Zoology (ZSM) in Munich. The ZSM is a key partner in the German Barcode of Life initiative and given the advanced stage of Barcoding Fauna Bavarica likely its largest contributor at this point. 

The second round of the project is divided into three work packages:
Work package 1: Filling the gaps in the current library by DNA Barcoding the remaining species. The project will shift focus to fungi, lichens, algae, diptera, red list species, FFH species (Fauna-Flora-Habitat directive of the EU), and neozoans. Also some efforts will be made to barcode old museum material (rare and extinct species).

Work package 2: Creating interfaces (through DNA Barcoding) between biology, medical sciences, forestry, agriculture and food production. This will specifically include indoor pathogens (e.g. fungi) as well as human/mammalian/vertebrate pathogens and parasites.

Work package 3: Offering digital and web-based portals to bring biodiversity information (as outreach for ongoing barcoding projects) to the public (especially schools and universities) and to the expert user including a digitization program for Bavarian collection material at the ZSM.

Of course I am proud to be a barcoder of German descent this week (and not only this week). After a stuttering start into the barcoding business with a lot of initial skepticism among researchers, Germany managed to become a leading country within iBOL and demonstrates that it is possible to jointly build state and country-wide reference libraries that are actually used.

Congratulations to the team in the Free State of Bavaria.

Tuesday, October 8, 2013

Award for German Barcoding Project

The Zoological Museum Alexander Koenig in Bonn, Germany has received the award 'Ort des Fortschritts' (site of progress) by the North Rhine-Westphalian research ministry. This award recognizes the work of the Leibniz Institute for Animal Biodiversity especially for coordinating and leading the German Barcode of Life Project (GBOL).

The North Rhine-Westphalian research minister Svenja Schulze says: Museum Koenig is a perfect match for this award that stands for sustainable research in Europe. The accumulated knowledge will help us to conserve and sustain resources for humanity. This is socio-relevant biological research that bridges fundamental research and application.

This price is awarded since 2011 and honors institutions or projects that combine Economy, Ecology and Society in an innovative way. Congratulations to the colleagues in Germany at large and specifically to the ones at the Museum Alexander Koenig.

Friday, October 4, 2013

Barcode library construction

As I am scrambling with last minute preparations for the upcoming online course I was extremely grateful when my colleague Rodger Gwiazdowski offered to write a guest post. So here we go:

Workflow of specimens from museum drawers,
into designed-for-DNA-Barcode-sampling
Schmidt boxes, and preliminary data capture.
DNA Barcode-based identifications depend on the taxon coverage of reference libraries. Museums are primary sources of specimens, and Dirk has blogged about this idea here before. As I help assemble a reference database for all Hemiptera native to Canada (~ 4K species of aphids, stinkbugs, cicadas etc.), I notice the biggest challenge is not finding all the species we need in museums, but obtaining barcode-compliant sequences from many species - mostly due to specimen age.

To address this, Paul Hebert and colleagues recently published predictive data on barcode-compliant sequence recovery from their large ‘Barcode Blitz’ across the ANIC Lep collection. Their findings affirm that museum sampling is the main tool for library construction. However, variation in specimen availability and age may require additional tools for comprehensive coverage.

As an example, the Canadian Hemiptera library still needs at least one specimen from 779 species across the Heteroptera (one of the four main Hemipteran suborders). I recently surveyed for all 779 in the Smithonian’s collection. Of these, ~290 were collected in the past 30+ years (many through curator Tom Henry’s additions/ID’s), and are likely to yield barcode-compliant sequences. About 80 species have their youngest specimens in the late 19th and early 20th centuries, and  ~320 species were not collectable as they were on loan, never accessioned or the very few specimens present (2-4) were preferred to be kept in-house (the vast majority were from the early 20th century, anyway). My observations, unfortunately, don’t include the valuable Carl John Drake Collection where specimens cannot be taken off-site - as a condition of the collection donation. On site, ‘Barcode Blitz’, sampling efforts have clear advantages here, but can’t address unavailable species, or those too old for barcodes.

Tingid specimens from the late 19th,
and early 20th centuries alongside recently
collected specimens to be DNA barcoded.
Hard-to-get species can be found through other museums, and a collaborator network. But the search can be expensive. All curators tell me if they don’t have recent specimens (as in, the past 30-50+ years), they’d like some. Because fresh specimens are ideal for barcoding, it seems possible to acquire rare taxa, and deposit them as vouchers using (at least) two new tools: DNA Barcoding at BioBlitzes and eBol.

Recently, ~ 5K specimens, collected during the world’s largest BioBlitz (Rouge Park, north of Toronto), will have their DNA Barcodes sequenced, and eBOL projects (curriculum based DNA Barcoding) are pairing students with taxonomists to analyze data using BOLD. As library construction efforts learn who their hard-to-get taxa are, regional BioBlitz participants can be alerted to look for these taxa, and students could take on sampling these species as an eBOL project. In both cases, citizen scientists, and educators could directly fill bioinformatics gaps in taxon libraries where vouchers reside in public collections.

Images were taken in the Smithsonian's Hemiptera collection, August 2013

Tuesday, October 1, 2013

Sharing, sharing, sharing

As I've mentioned it in a couple of blog posts before I am a big proponent of open access. Not only for any sort of publication but also for data generated through research. Data and information sharing makes all our lives as researchers easier.

The early release of DNA sequence data is common practice in some communities, e.g. genome projects do that on a regular basis and it becomes the rule rather than the exception that the community works on the annotation of the data. Unfortunately, in the barcoding community this is not common practice and many colleagues would like to have rather more time to work with their data before releasing them. There are a variety of reasons for that reaching from being afraid to be scooped by overly competitive colleagues all the way to the fear to be embarrassed for providing wrong annotations (identifications in our business) in the first place. In the latter case a more reasonable concern seems to be the fact that wrong ID's would pollute any database such as BOLD and in some instances provide wrong identifications. Indeed this could lead to some serious error propagation which is a phenomenon long known from GenBank. However, diligent work and data maintenance of barcode data owners can certainly overcome this and BOLD offers a variety of tools to help with data curation and cleansing.

Maybe the results of a new study published in PeerJ help to overcome some of those concerns as it points out the advantage of open data. Two researchers from Duke University looked at gene expression publications between 2001 and 2009 and calculated that on average studies with publicly available data are cited about 9% more often than others. It seems to pay off to have data out there in the public. In addition the study shows that researchers tend to use their own data on average for to two years after initially publishing them. Their colleagues often refer to them up to six years after data went public.Overall the number of datasets used for a single publication went up from 1-2 in the years 2002-2004 to 3 and more in the year 2010.