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!

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.

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.

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

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.

New cool journal

A new open-access journal started mid September and it promises to fill a void in the current publication space. I have written about data release papers before and it seems the perfect outlet for such has just been created from the publishers that are responsible for ZooKeys (the open-access competitor of ZooTaxa):

Biodiversity Data Journal (BDJ) is a community peer-reviewed, open-access, comprehensive online platform, designed to accelerate publishing, dissemination and sharing of biodiversity-related data of any kind. All structural elements of the articles – text, morphological descriptions, occurrences, data tables, etc. – will be treated and stored as DATA, in accordance with the Data Publishing Policies and Guidelines of Pensoft Publishers.

The journal will publish papers in biodiversity science containing taxonomic, floristic/faunistic, morphological, genomic, phylogenetic, ecological or environmental data on any taxon of any geological age from any part of the world with no lower or upper limit to manuscript size. For example:

• single taxon treatments and nomenclatural acts (e.g., new taxa, new taxon names, new synonyms, changes in taxonomic status, re-descriptions, etc.);
• data papers describing biodiversity-related databases, including ecological and environmental data;
• any kind of sampling report, local observations or occasional inventories;
• local or regional checklists and inventories;
• habitat-based checklists and inventories;
• ecological and biological observations of species and  communities;
• any kind of identification keys, from conventional dichotomous to multi-access interactive online keys;
• descriptions of biodiversity-related software tools.