Wednesday, March 27, 2013

Ultra-deep sequencing

Next generation sequencing in biodiversity research usually involves DNA extraction of bulk samples, PCR amplification of targeted markers and subsequent massive parallel sequencing. Those bulk samples can contain entire organisms or come from a single environmental sample containing degraded DNA. A drawback in this procedure is the PCR amplification step that is applied to acquire a sufficient number of barcode sequences. Primers are designed to amplify a large range of taxa present in the bulk sample but those are rarely universal. Although much effort has been made to increase the universailty and efficiency of primers it is difficult to predict their performance when an investigated fauna is largely unknown.

A group of researchers from the Beijing Genomics Institute have developed a new pipeline that is independent of PCR amplifications while still enabling DNA Barcode identification. They used ultra-deep sequencing to detect minute traces of mitochondrial sequences directly from genomic DNA mixtures.

For this proof of concept study 73 insects were collected, preserved and visually identified. Once complete (as far as possible) DNA from the legs of each creature was analyzed using DNA barcoding (with standard Sanger sequencing) and compared with data from the Barcode of Life Data Systems. Subsequently, after mitochondrial enrichment using differential centrifugation, total genomic DNA was extracted from a homogenized mixture of the remainder of the insects.

The group employed two different approaches to assign species-level identity: 
(1) By utilizing a DNA Barcode reference library for the investigated fauna. Sequence reads were mapped to the reference sequences following defined criteria.
(2) In absence of a reference library, a de novo assembly of sequence reads into mitochondrial gene fragments, especially the COI Barcode region, was employed, followed by gene annotation, to ensure accurate detection of taxa from the mixed bulk sample.

Both experiments worked quite well which I find very exciting. The team was able to assess biodiversity at the species level regardless of whether a species can be actually named. Their work also showed that it is possible to calculate the total quantity of mitochondrial DNA present which would allow to extrapolate the ratios and physical mass of each species in the mix.

Of course this proof of concept needs to be transferred into 'real-world' applications but once working it would represent a big step forward for biodiversity-related surveillance efforts, such as in biomonitoring programs.

Tuesday, March 26, 2013


Paragonimus life cycle
Paragonimus is a genus of flatworms which causes human paragonimiasis. Contraction of paragonimiasis usually occurs when humans eat undercooked freshwater crustaceans, such as crabs or crayfish. These often contain  metacercariae which are intermediate forms of the flatworm. Once ingested and in the intestine, the parasite will move into the guts and into the lungs. In the lung, the parasites transform into a cyst where they will cross fertilize with one another. The cyst will rupture in the lungs and eggs are either coughed up or swallowed and excreted through feces. Eggs landing in the freshwater will hatch and  infect the first intermediate host which is usually an aquatic snail. A crustacean may also become infected by eating the infected snail. The cycle starts again when the definitive host (e.g. the human) ingests the infected crustacean.

Symptoms of paragonimiasis include abdominal pain, diarrhea, fever, and hives. These symptoms can last for months and sometimes even up to 20 years. Most symptoms are caused by the body’s natural immune response to presence of the worms and eggs and their migration from the intestines to the lungs. On average, it takes about eight weeks for the parasites to start producing eggs in the lungs but only three weeks to develop symptoms,

Paragonimus mexicanus is the causal agent of human paragonimiasis in several countries of the Americas. It is considered to be the only species of the genus present in Mexico, where it is responsible for most human infections.

Mexican researchers have now investigated Paragonimus mexicanus specimens from several locations in Mexico. The provide conclusive morphological, molecular (DNA Barcodes) and geographical evidence that strongly suggest the presence of at least three species in Mexico. One of the three species is likely new to science and another one could be one (Paragonimus ecuadoriensis) that was considered a junior synonym of Paragonimus mexicanus. 

These results have important implications with respect to diagnosis, treatment, and control of human paragonimiasis in Central America. There are more than 50 species described in the genus and nine of them are from the Americas. The authors clearly state that the taxonomic status of some of these species also needs to be reinvestigated to establish the number of causative agents of human paragonimiasis.

Monday, March 25, 2013

High School Students test beef products

guest post by Ralph Imondi
Mini Food Authentication Study Conducted by California High School Students Finds No Evidence of Horsemeat DNA in Beef Products

In the wake of the recent European horsemeat scandal, high school seniors working at Ventura-based Coastal Marine Biolabs (CMB) took a brief diversion from building the BOLD reference library to examine the contents of beef products sold at local supermarket chains, health food stores, membership warehouse clubs, fast-food restaurants, and a foreign company better known for its ready-to-assemble urban furniture than for its food markets and restaurants.  A team of 4 students collected a total of 32 food products that included ground beef, shaved steak, cooked and uncooked beef patties, and meatballs. Upon returning to the CMB lab, they then applied DNA Barcoding to detect the presence of horsemeat in each product.  In stark contrast to the results obtained from DNA-based testing of European meat products, the students found no evidence of horsemeat in any of the samples examined with DNA barcoding.  Instead, their testing detected only domestic cow (Bos taurus) DNA in 29 products labeled as 100% beef, and a combination of both domestic cow and pig (Sus scrofa) DNA in 2 products labeled as containing both beef and pork.   
FoothillTechnology High School seniors Jongseung Baek, Eric Moll, Emily Park, and Amanda Torres conducted the 5-day food authentication study as an extracurricular science project.  Earlier in the semester, these same students and their classmates assembled a series of BOLD-compliant reference DNA Barcode records for groundfish species collected during the third leg of a NOAA-sponsored trawl survey, which was conducted in summer 2012 around Alaska’s Aleutian Islands.  Both student-led efforts were carried-out in connection with the NSF-funded Barcoding Life’s Matrix program hosted by CMB.

According to Emily Park, one of the team members involved in the projects, “participating in the DNA barcoding initiative, both in the classroom and at Coastal MarineBiolabs, allowed me to do research that has influence outside of  just a local, school context. Not only did I use science for class work, I could contribute to an international database tied to biodiversity conservation and even consumer fraud. It's cool to know that the concepts you learn in DNA barcoding have direct applications in real-life, and that even high school students can take part in that direct application.”

Saturday, March 23, 2013

Deadly reproductive habits

Most of the parasitoid wasps of the family Braconidae have some deadly reproductive habits. Their eggs develop in other insects and their larvae, eventually killing the respective host, or in some cases immobilizing it or causing its sterility. The family is also very diverse with estimates as high as 150,000 species. Now three new species of the genus Cystomastacoides are described and the authors demonstrated some creativity when they named the species. 

The genus has been known only from a single species, Cystomastacoides coxalis, which was found only in mainland China (Yunnan). Two of the new species were discovered in Papua New Guinea, while the third one comes from Thailand. The Thai species, Cystomastacoides kiddo, was named after the character Beatrix Kiddo in Quentin Tarantino's 'Kill Bill' films. The deadly biology of the wasp inspired this reference to the protagonist played by Uma Thurman, where she embodies a deadly assassin and a master of the Tiger/Crane style of kung fu. She is a master of the "Five Point Palm Exploding Heart Technique", a method of killing a person by quickly striking five pressure points around the heart with the fingertips. After the victim takes five steps, the heart explodes and the person falls dead. Now we're talking.

The macabre in the name of one of the new species from Papua New Guinea references back to another strand of contemporary pop culture: Cystomastacoides nicolepeelerae is named after Nicole Peeler, the favourite novelist of Donald Quicke, the lead author of this article. Nicole D. Peeler is an American author who writes the Jane True - Tempest urban fantasy series.. Apparently she is very happy about the honor:
Cystomastacoides nicolepeelerae

And it’s a big deal to me, because it’s AWESOME. Not least because my wasp is a “parasitoid wasp,” known for its “deadly reproductive habits.”

The name of the third species, Cystomastacoides asotaphaga, also from Papua New Guinea, lacks the popular culture element but still brings up the deadly survival techniques of the wasps described. In translation, it means feeding on Asota, a genus of moths whose caterpillar is eaten from the inside by the wasp's larva and thus eventually killed. Asota plana is the first host record for the genus to which the new species belong. It is a widespread moth species known to feed on multiple fig tree (Ficus) species.

Thursday, March 21, 2013

Tiny Minotaurs and a subgenus of Mini-Casanovas

Nepticulidae is a family of very tiny moths, with wingspans of 3 to 8 millimetres. These pigmy moths or midget moths have evolved more than 110 million years ago. Australian pigmy moths are particularly diverse and unusual, and one group (genus Pectinivalva, 'ancient pigmy moths') has until now only been reported from that continent, where over 140 species are known. Each species of pigmy moth is associated with one or a few related species of plant on which they lay their eggs. Caterpillars make a mine inside the leaf, the shape of the mine often being characteristic of the species that made it.

By reconstructing the evolution of the ancient pigmy moths, Researchers Robert Hoare (Landcare Research, New Zealand) and Erik van Nieukerken (Naturalis Biodiversity Center, Netherlands) have now shown that the original host of the group was probably a rainforest plant of the myrtle family (Myrtaceae). As Australia dried out from about 15 million years ago, the rainforest was greatly reduced in extent, and the myrtle family came to dominate the vegetation of the arid interior, with the now familiar eucalyptus trees becoming especially diverse and abundant. The ancient pigmy moths in their turn transferred to the newly dominant host-plants, and now most known species of Pectinivalva feed on Eucalyptus and its close relatives, with just a few still attached to rainforest myrtles. Probably, the rainforests of Indonesia, New Guinea and New Caledonia will be found to be home to further undiscovered members of this genus; a new species (P. xenadelpha) from Borneo is the first non-Australian member of the genus known.

Male Pectinivalva minotaurus
The authors also showed some creativity when it came to naming new species. One moth was named after the Minotaur of the Greek mythology. The male of one of the most spectacular species has huge flattened and expanded antennae, whose function is unknown, but which are also presumed to be attractive to females. This species has been named Pectinivalva minotaurus, after the bull-headed Cretan beast of Greek mythology. 

The males of many species of ancient pigmy moths display special scales for close-range scent dispersal during courtship of the female. These can be on the front legs, on the wings or on the body of the moth, and may form moustache-like tufts or groups like overlapping shells. Some species have a strange pocket-like structure on the hind wing with scent scales surrounding it in a palisade. In one group of metallic-coloured species, the males are particularly well equipped for courtship with a variety of sex-specific modifications. This group has been named as a subgenus Casanovula after Giacomo Casanova, the Italian adventurer famous for his many romantic entanglements.

From BOLD to TV

I am sure that many but not all of you know that the database and workbench for DNA Barcode data - BOLD - is also a huge repository for specimen images. Many - unfortunately not all - records on BOLD contain at least one image of the specimen that has been barcoded. The main idea is to enable researchers such as taxonomists to communicate with each other on identifications that are based on morphological differences. In many cases such an image was enough to solve uncertainties in identifications thereby avoiding the shipment of a specimen for comparative work which is costly and always a little risky.

click to enlarge (Photo Vanessa Bouwer)
Images of a record are publicly available and indexed with the big search engines. I see them coming up more and more in Google image searches. This results in some unexpected attention by the media. Recently the team of the Dr. Oz Show contacted us as they found an image on BOLD's taxonomy browser which they wanted to use for a show on parasites. The actual owner of the image was quickly found and yesterday the show was aired.

I am not a big fan of TV shows that exaggerate risks and danger of sickness. Have a look at the trailer and you know what I mean. Don't get me wrong - as far as I know the Dr. Oz show usually does a reasonable good job to explain health issues and how to deal with them. However, this parasite episode overshoot the mark a bit by dramatizing the prevalence of parasites. On the other hand some of the dietary recommendations they make in the show are not bad at all. There is no harm in eating more fiber or garlic for many reasons. I am convinced those are very healthy alternatives but I don't know enough about parasitology to judge if they are also good parasite remedies.

Nevertheless, great to see that the work of colleagues is shown and that they get credit for it. Last year a graduate student at the Natural History Museum in Buenos Aires was contacted by National Geographic Learning. One of his spider photos they found on BOLD made it into a textbook to teach English to children at the primary level around the world. The books have a strong focus on science, nature, and the environment.

And what's the take-home-message of all this?
Don't forget to upload images for all your BOLD records and provide licensing information on them. You never know who might call tomorrow.

Monday, March 18, 2013

Up on the roof

Green roofs have become increasingly popular in urban sustainability initiatives, as they provide a number of ecosystem services that mitigate the effects of urbanization such as decreased storm water runoff, enhanced building energy-use efficiency, and reduced urban heat island effects. However, little research has been done on the biodiversity of those communities especially the non-plant biota associated with green roofs, which likely affect their functionality. 

In a new study, a group of US researchers evaluated whether or not green roofs planted with two native plant communities in New York City functioned as habitats for soil fungal communities, and compared fungal communities in green roof growing media to soil microbial composition in five city parks

Sampling schemes for soil cores
The reserarchers utiilzed massive parallel sequencing of the fungal DNA Barcode region (ITS) and found that green roofs supported a diverse fungal community, with numerous taxa belonging to fungal groups capable of surviving in disturbed and polluted habitats. Across roofs, there was significant biogeographical clustering of fungal communities, indicating that community assembly of roof microbes across the greater New York City area is locally variable. Green roof fungal communities were distinct from city parks and only about half of the green roof taxa were also found in the park soils.

While fungal communities were compositionally distinct across green roofs, they did not differentiate by plant community. Together, these results suggest that fungi living in the growing medium of green roofs may be an underestimated component of these biotic systems functioning to support some of the valued ecological services of green roofs.

Understanding how biodiversity is assembled and maintained will be useful for managing green roof systems to maximize their provision of ecosystem services while simultaneously minimizing external inputs and roof maintenance. In addition to their practical aspects, green roofs that represent vegetated islands can also function as ideal experimental systems for asking ecological questions about community assembly and habitat fragmentation .

Friday, March 15, 2013

BOLD Student Data Portal

For regular readers of this blog it is not news. The BOLD team has released a Student Data Portal designed to open the world's leading DNA Barcoding database and workbench to the classrooms. Today they also released a nice video to promote the new interface. You should have a look as it is really very well done:

Open Access - on a personal note

I have repeatedly voiced my support for open access of scientific publications in this blog and I am sure I will continue to do so.

However, there are obviously some misdirected people out there (it is hard to refrain from name calling!) that thought it is a good idea to use my university account to access our university library remotely to download large numbers of publications.

(1) I have no idea how they managed to hack into my account as I never react to any phising attempt and I am very protective of my passwords. However, I also know that nothing is really safe in the web.
(2) I don't know what the motivation for this was but it is either greed (maybe one can sell the papers somewhere else) or even worse somebody who thought this is the best way to make publications accessible to the public.

My message to this nutcase(s) somewhere in Germany (that's where the IP's point to) is to hold on for a minute and think about it. You are breaking into someone's account in order to break into a university library! Double illegal and most cowardly. If it is really about open access stop hiding and refrain from causing trouble to others.

Thursday, March 14, 2013

Did you know the BOOK?

I have to admit that I do own an eBook reader and I use it most of the time as opposed to grab a BOOK. 
Nevertheless, this is a great video about a 'new' invention with all available accessories (or should I rather call it a necessary reminder?). Enjoy a funny 3:20 sales pitch (in Spanish with English subtitles):

Toyota Enviro Outreach 2013

Toyota Enviro Outreach team 2012
I usually try not to provide free ads for companies but this very successful program sponsored by Toyota South Africa and other corporations surely deserves a post.

Already for the fifth time a team of South African researchers will use a small fleet of vehicles (you can guess the make of those) to travel to a remote site in South Africa to collect samples for DNA Barcoding. 

This years tour will start on April 2nd at the Klipbokkop Mountain Reserve and will run until April 14th, during which time scientists and students from the University of Johannesburg, the South African National Biodiversity Institute, University of Pretoria, and University of Cape Town will visit several floristically interesting sites in the extremely arid Gariep region (Gariep Desert, Bushmanland Inselbergs, quartz patches) and the Upper Nama-Karoo region of the Northern Cape Province, with the goal to collect material for herbarium specimens and DNA Barcoding, as well as information about species distributions, population surveys of threatened species, habitat and threat assessment data while also recording information about plant utilisation.

South Africa is home to almost 10% of the world’s plant species and an astonishingly rich faunal diversity. It is paramount to learn more about this diversity otherwise the country would be limited in its ability to use such a national asset to solve environmental and human welfare challenges. Furthermore, with the current rate of extinction no other generation will have access to the number and diversity of species that we have now (many of which still remain unknown to science). It is the mission of the African Centre for DNA Barcoding (ACDB) is to bridge this knowledge gap and strengthen research frameworks for international, regional and inter-institutional co-operation in Africa. The ACDB collaborates with the International Barcode of Life project (iBOL) to explore the resources of South Africa's biodiversity, especially species that are poorly known. They are therefore extremely important and their preservation for future generations pivotal. 

Happy collecting!

Wednesday, March 13, 2013

Citizen science surveys compare well with traditional scientific methods

Research published today in Methods in Ecology and Evolution shows that methods to record marine diversity used by amateurs returned results consistent with techniques favoured by peer-reviewed science. 

The findings give weight to the growing phenomenon of citizen science, which sees data crowd-sourced from an army of avid twitchers, divers, walkers and other wildlife enthusiasts.

The field study compared methods used by 'citizen' SCUBA divers with those used by professional scientists, to measure the variety of fish species in three Caribbean sites close to South Caicos in the Turks and Caicos Islands.

Locations of survey sites used for the comparison
The divers surveyed the sites using two methods -- the 'belt transect', used in peer reviewed fish diversity studies, and the 'roving diver technique', used by the Reef Environmental Education Foundation (REEF) volunteer fish survey project.

Two teams of 12 divers made 144 separate underwater surveys across the sites over four weeks. While the traditional scientific survey revealed sightings of 106 different types of fish, the volunteer technique detected greater marine diversity with a total of 137 in the same waters. The larger number of species detected by the volunteer protocol suggests this protocol may be advantageous with regards to the completion of taxonomic lists.

Dr Ben Holt, from the University of East Anglia, led the research in partnership with the Centre for Marine Resource Studies in the Caribbean and the University of Copenhagen, Denmark. This is what he said in a press release:

The results of this study are important for the future of citizen science and the use of data collected by these programs. Allowing volunteers to use flexible and less standardised methods has important consequences for the long term success of citizen science programs. Amateur enthusiasts typically do not have the resources or training to use professional methodology. Our study demonstrates the quality of data collected using a volunteer method can match, and in some respects exceed, protocols used by professional scientists. Enlisting the help of a large pool of volunteers helps professional researchers collect valuable data across many ecosystems.

The popularity of SCUBA diving has resulted in monitoring of the underwater environment on a scale that was previously impossible. For example, the REEF method has been used by volunteers in more than 160,000 underwater surveys across the world. It would have cost many millions of pounds for professionals to have undertaken the same work.

For example Lion fish is an invasive species which was not in the Caribbean until roughly 10 years ago. They have now become a real problem in many areas and this invasion has been tracked using volunteer data. Following our study, scientists can have more confidence when using these data to consider the impact of threats, such as invasive species, on the wider natural communities.

It is important to note that our study does not consider the abilities of the individuals performing the surveys and this is also an important consideration for any large scale biodiversity program. By addressing these issues we can make important steps towards enabling the large pool of volunteer enthusiasts to help professional researchers by collecting valuable data across many ecosystems.

Tuesday, March 12, 2013

A new fish - an old problem

The genus Alburnoides belongs the large carp family Cyprinidae that includes freshwater fishes such as he carps, the minnows, and their relatives. This is the largest fish family, and more notably the largest family of vertebrate animals, with over 2,400 species. Cyprinids are highly important food fish because they make the largest part of biomass in most water types except for fast-flowing rivers.

X-Ray for Alburnoides manyasensis
The genus Alburnoides is widely distributed in Turkey in rivers and streams of basins of the Marmara, Black and Aegean seas, being absent only from the Mediterranean Sea basin. Now, a new species Alburnoides manyasensis, is described from the Koca Stream drainage of Lake Manyas, Marmara Sea basin in Anatolia and it is currently only associated with this specific locality. The name of the species is an adjective that is derived from the name of Lake Manyas to which the new species is possibly endemic.

The new species inhabits clear fast running water with cobble and pebble substrates. It is a comparatively small representative of the family with maximum known body length of only 92 cm while the largest representative of the family, the giant barb (Catlocarpio siamensis) can reach up to 3 m in length.

A quick look at BOLD showed me that 36 barcode sequences of the genus Alburnoides are in the database but only 18 are public. Most of them have been identified as Alburnoides bipunctatus but a quick NJ tree of the public sequences showed three clades separated by relatively deep divergence. That could be an indication of species but without a closer look at actual specimens and more information I will refrain from jumping to any conclusion. However, if there are several species hiding under one name it would be very important to find out if they are already known to science or not. This is of course only possible if the DNA Barcode library is complete.

Localities for barcoded specimens of the genus Alburnoides
When I read all these new species records I always wonder why in most cases such as for Alburnoides manyasensis they are not assigned a DNA Barcode as soon as they are described. I am well aware that not everybody has access to a sequencing facility and that there probably aren't sufficient funds to do that but it would at least be a goal worth aiming for. An initiative to generate DNA Barcodes for all species described in the years to come. It would need money but who says that there aren't any potential funders that like the idea. However, it would also need the taxonomic community to provide smallest tissue bits from their type material. That is probably far more complicated to accomplish although no voucher would be damaged. It still seems to be very hard for some taxonomists to share a piece of a specimen especially with the DNA guys.

At this point the researchers who described Alburnoides manyasensis assume that it potentially represents an endemic species. Maybe it is not and we might even have some barcoded specimens registered under a different in this case wrong name. I am afraid we might not be able to find out as it is still common practice in many collections to preserve specimens in formalin. The type specimen (and the paratypes) might be already lost for any DNA-based research.

Monday, March 11, 2013

Barcoding parasitic worms

Acanthocephalan with hooks
Acanthocephalans are intestinal parasites of vertebrates. Adult endoparasites inhabiting the digestive tract of  fish, marine mammals, birds amphibians, and reptiles. Larval development takes place in intermediate arthropod hosts typically crustaceans (amphipod, copepod or decapod). Human infections are considered to be rare

The name "Acanthocephala" is derived from Greek roots meaning "spiny head" and refers to the set of hooks on one end of the worm. Most acanthocephalans are less than 20 cm long, although a few exceed 60 cm. Females are generally larger than males. As a consequence of their lifestyle, the digestive tract has been completely lost and most other organ systems are notably reduced, with the exception of the reproductive system.  

Acanthocephalan cystacanth in an amphipod
The life cycle of most species is poorly understood but, apparently, eggs are released from the definitive hosts with the faeces. Once in the water, eggs are eaten by an arthropod that represents the intermediate host, where up to three larval stages are developed (acantor, acanthella and cystacanth). Aquatic vertebrates (such as fish) feed upon the arthropods and the last larval stage the cystacanth re-encysts. The life cycle is completed when these hosts are eaten by other vertebrates (e.g. fish-eating birds) and the adult parasites establish in their intestines.

Similarly to other endoparasites the taxonomy of acanthocephala is based on adult morphological traits. Larval forms cannot be assigned to species. As a result we have only little understanding of the life cycle of most parasite species let alone what their hosts are.

A group of Mexican Researchers has now shown how DNA Barcoding can help to assign larval stages to adult forms. They successfully linked larval stages of the acanthocephalan species Polymorphus brevis found in freshwater fishes with adults that usually parasitize other aquatic and terrestrial vertebrates, most commonly fish-eating birds. They sequenced cystacanths from freshwater fishes collected across central Mexico and adults obtained from fish-eating birds, to determine whether they were conspecific. To corroborate the molecular results, they conducted a morphometric analysis using a software developed to detect heterogeneity in otherwise morphologically similar acanthocephalans based on the multivariate statistical analysis of hook dimensions. Both methods showed that larvals stages infecting freshwater fishes in central Mexico belong to a single species, Polymorphus brevis. 

...the development of a library of COI sequences will be a valuable resource for better understanding the life cycles and intermediate and definitive host spectra for helminths (parasitic worms) across large spatial scales, and a broad variety of host taxa. 

Dirk Steinke (2013). Barcoding parasitic worms

Thursday, March 7, 2013

Reader's Digest February 2013

A new Barcode Bulletin Reader's Digest just went out to all subscribers.

This time I also created a RIS format file in case readers want to add the citations to their reference management software. RIS files are usually work best across all platforms. I am also working on a Mendeley version of my entire DNA Barcoding library. Stay tuned.

Here are the links:
Good old fashion pdf with hyperlinks
RIS format file

5th International Barcode of Life Conference

So far you have probably heard only rumors and saw a small announcement but now it is official. After London, Taipeh, Mexico City, and Adelaide, Kunming will be hosting the Fifth International Barcode of Life Conference.

Organizers are the Kunming Institute of Botany, Chinese Academy of Sciences (CAS) and Kunming Institute of Zoology, CAS. The conference is co-hosted by iBOL and the iBOL China National Committee. The conference will be from 27-31. October 2013.

DNA barcoding has come a long way since December 2011 when we met in Adelaide for the Fourth International Barcode of Life Conference. The 2013 conference will provide an opportunity for delegates from around the globe to showcase and discuss scientific advancements in DNA barcoding and the wide-ranging socio-economic applications developed since the Adelaide Conference, and to review the progress in this field over the past decade. The Kunming conference will bring barcode researchers together to exchange ideas and plan new activities, and to learn about barcoding activities in China and the region. The theme of the conference is “Global Change and the Barcode of Life: Opportunities and Challenges”. The conference will be held at the Lian Yun Hotel near Green Lake with a stunning view of Kunming. There will be two days of pre-conference workshops, including full-day short courses that will introduce participants to the lab protocols of DNA barcoding and to the management and analysis of barcode data. The week of events will culminate in a barcoding event for the public in the Kunming Botanic Garden of KIB.

So this time the DNA Barcoding world meets in the "City of Eternal Spring" and the "Capital of Flowers". Kunming's history dates back more than 2000 years. Once a major textile distribution center on the Southern Silk Road it is now the fourth largest city in Western China and the political, economic, and cultural center of the Yunnan province.

Registration and abstract submission will start soon. A call for papers, symposium and workshop proposals will come out in a few days. I don't know what the venue capacity is but the organizers stress that it will be limited, so better register sooner than later.

I am a member of the scientific program committee and will post any news and important updates as soon as I learn about them.

Wednesday, March 6, 2013


PestBOL web resource
Today a new DNA Barcoding web resource went live. The Plant Pest Barcoding site provides summary information on DNA Barcode coverage for invertebrate pests of significance to global plant production. It is intended for use by the plant protection community, including regulators, researchers, and growers. By highlighting gaps in coverage, it also supports coordinated efforts to further the development of DNA Barcode reference libraries for pest arthropods.

The majority of described species are invertebrates, approximately 1 million in all, with hundreds of thousands more awaiting description. As a result of their sheer numbers, varied life-stages and diverse life-history strategies it can be extremely challenging to identify invertebrates to species. Unfortunately, this hinders our ability to cope with invertebrate pests at all management levels, from growers to governments. DNA barcoding critically extends our ability to detect pests but its application is predicated on the existence of a barcode reference sequence library derived from expert-identified reference specimens held in accessible museum collections.

What I find worth mentioning is the fact that that to a large extend this resource is the result of the work of one person, Andrew Frewin, a PhD student at Bob Hanner's lab at the University of Guelph. He gathered information on species from various sources including national and international pest lists, and merged both regulated and non-regulated pest species into a global checklist. The single criteria for inclusion of a pest species in this list was the occurrence of that pest on a national or international pest list, or in an academic or industry report

Take home message is that it just takes the dedicated effort of less than a handful of people to build a resource that will likely have a very big impact due to it's societal relevance. 

The other good news is that based on the current iteration of the list (and it will be updated over time) 358 agricultural pest species have a DNA Barcode. That is 40% of the list. In my opinion that is a huge step forward and opens the door to modernization of pest detection and pest control.

Tuesday, March 5, 2013

Video for science bloggers

Even if you don't like the music and the hype around Psy this video is fun to watch.

It was created by Carin Bondar featuring attendees of this years ScienceOnline conference. ScienceOnline is a non-profit organization that facilitates conversations, community, and collaborations at the intersection of Science and the Web. You can guess why I find that very interesting. I came across the video on

Monday, March 4, 2013

2 Million DNA barcodes

Last Friday more or less on the q.t. BOLD surpassed the 2 Million sequence mark.

This is quite an accomplishment for the young discipline DNA Barcoding especially given the amount of collateral information connected to every record. However, the International Barcode of Life Project (iBOL) has much greater goals. Until 2015, iBOL participants want to gather DNA barcode records from five million specimens, representing at least 500 000 species. More than a million sequences have been added to the barcode library since the launch of iBOL in 2010. It is obvious that work needs to be scaled up to reach the five million target by the end of 2015.

What seems to be already within reach is the goal to barcode at least 500 000 species by 2015 as there are now records for more than 300 000 barcode clusters of plant and animals.

After seeing these number I was immediately interested in more details. I obtained some numbers from BOLD's taxonomy browser to calculate the taxonomic breakdown of the formal species barcoded. The result - two simple pie charts depicting coverage of animal phyla and plant divisions:

Formally described animal species with DNA Barcodes on BOLD
It is not surprising that more than 3/4 of all formal animal species with a DNA Barcode are arthropods. Not only is it the most speciose phylum in the animal kingdom but also the target of a lot of DNA Barcoding activities such as the campaign to barcode all lepidoptera.

What is nice to see is that other groups are catching up. One example are the chordates. To this date the library contains a third of all known fish species and amphibians respectively, almost half of each the birds and the mammals, and a quarter of the reptilians. The recent announcement that CBOL has been granted funds from Google to barcode a large number of endangered animals lets me believe that these numbers will likely go up rapidly.

Formally described plant species with DNA Barcodes on BOLD
Another impressive figure shows the progress of plant DNA Barcoding. Let's not forget that the formal acceptance of the rbcL and matK chloroplast genes as DNA Barcodes for land plants dates back just 4 years. 13% of the known green plant species have been added to the DNA Barcode library.

Within 10 years we have amassed DNA Barcode records for more than 10% of all described species. Now that is quite an accomplishment!

Friday, March 1, 2013

School Malaise Trap Program Week 1

Week one has come to a close. Here some impressions from the school visits we had:

The BIObus is coming

Line up for a peek into the field vehicle

The entomologist's workplace
How an aspirator works - and yes, we don't suck the bugs into our mouth.
An introduction to DNA Barcoding for Grade 6 students
More bugs!