Monday, December 24, 2012

Enjoy the Holidays!

No posts for a few days as I am going to have some family time without work. 
I wish everyone a wonderful Christmas time and a happy, prosperous, and healthy new year.
This blog will resume in January 2013 - Meanwhile I'll keep collecting interesting news for you.

It was a great year 2012 which also saw the successful start of this blog. 
Thanks to everyone for being part of the journey as readers.

Friday, December 21, 2012

new iBOL Bulletin

Lot's of work over the last few days and here the result. The new iBOL Barcoding Bulletin.
Enjoy reading (just click on the image and it will open the pdf).

Thursday, December 20, 2012


Over the years the number of plants being traded worldwide increased and with that the chance of harmful organisms spreading was greatly enhanced. At the same time, the taxonomic knowledge available to identify harmful quarantine organisms via their visual characteristics decreased gradually.

The resulting economic damage is significant and shows how vital the development of accurate identification tools for plant pathogens and pests is.

Three years ago researchers from 15 mainly European nations founded QBOL a project financed by the 7th Framework Program of the European Union with the aim to make collections harboring plantpathogenic quarantine organisms publicly available. One main goal was to sequence genes from selected species on the EU and EPPO relevant lists . Over the 3 years the sequences, together with taxonomic features, were included in an internet-based database system called Q-Bank

Some 18 000 sequences are available on the database and serve as identification and detection reference for phytosanitary organizations such as national plant protection organizations, general inspection bodies, and private laboratories. The project officially ended in September 2012 but the database will be continuously maintained and curated. However, as usual funding is not unlimited and similar to all other databases out there Q-Bank is looking for more suistainable solutions.

Good luck!

Tuesday, December 18, 2012


Phytoplasmas in a phloem cell of a plant
Phytoplasmas are bacterial plant pathogens that cause significant losses in agricultural production worldwide. They are causing a wide variety of symptoms that can range from mild yellowing to the death of infected plants. They are most prevalent in the tropical and sub-tropical regions of the world. Phytoplasmas are transmitted by hemipteran insect vectors such as leaf hoppers, in which the bacteria are also able to survive and replicate.

Phytoplasmas infect over 200 plant species, prominent examples are coconut, sugarcane, and sandalwood. They are are considered of quarantine relevance e.g. in the EU, which means that their spread is especially tightly regulated. There are no fully resistant crop varieties currently available. Therefore, main disease management strategies are limited to control of the vectors provided that those are known, and the elimination of infected plants. There is a great need for reliable and efficient methods for identification for this group of pathogens, and our standard barcoding regions are likely inefficient.

Witches' broom caused by Phytoplasmas
A group of European researchers tested a set of primers amplifying a fragment of the so-called tuf gene (Elongation factor Tu) for their potential to serve as a DNA barcode for phytoplasmas. Elongation factor Tu is a key protein involved in the process of protein biosynthesis. Standard in DNA-based bacterial identification is 16S rRNA. Analysis and alignments showed that important groups of phytoplasmas could readily be identified. While being shorter, the tuf barcode provided clear resolution at both group and subgroup levels compared to the 16S rRNA gene making it an ideal candidate.

This work was part of the QBOL initiative, which aims to develop a DNA barcode-based identification system for pests and pathogens with a focus on quarantine organisms. The project has started to release data in a specific database - q-bank.

Monday, December 17, 2012

Get up, stand up

My apologies for not posting as often as usual but first I caught a pretty nasty bug and stayed in bed for two days and this week we are working on the finishing touches of the new iBOL Barcode Bulletin that should come out at end of this week. That work keeps me quite busy. Nevertheless, here a little story about a little newly discovered skipper butterfly that was found on Jamaica

Troyus turneri
Researchers from the Florida Museum of Natural History used morphology, especially comparisons of the insect's genitalia, and DNA Barcoding to determine that it was not only a new species but represented a new genus. Troyus turneri is a small butterfly with a wingspan of little more than 1 cm but according to some of the authors has the potential to be a flagship species for Jamaican habitat conservation, because it's a black butterfly with gold stripes living in a green habitat, which together comprise the Jamaican national colors. The resaerches hope the native butterfly will encourage conservation of the country's last wilderness where it was discovered: the Cockpit Country. It is the first butterfly discovered in Jamaica since 1995. The island was thought to be well-known, but now 17 years later the new encounter really shows the need for biodiversity studies in the region.

The genus was named Troyus for the town of Troy, which is nearest to the region of the Cockpit Country where it was collected, and the species was named for Thomas Turner, an expert on Jamaica butterflies who contributed to its discovery.

In case of further species discoveries in this genus may I humbly suggest names such as Troyus marleyi or Troyus toshii :-)

Thursday, December 13, 2012

Teleiopsis paulheberti sp. nov.

In no other field of research DNA Barcoding had more impact than in the taxonomy of lepidoptera. One of the first major papers was on some cryptic species of skipper butterflies, the order with the most barcodes to date (391353 representing at least 15865 species) is lepidoptera, and 157 papers on lepidoptera barcoding have been published since 2004 .

There is one more publication since Tuesday and what makes it perhaps more special that the others is the fact that the authors Peter Huemer and Marko Mutanen used it to honor the "Father of DNA Barcoding", Paul Hebert by naming a newly discovered alpine species after him. 

Teleiopsis paulheberti sp. nov. is described as follows:
Head cream-white; second segment of labial palpus cream-white, brown at base and apex, and tinged brown medially; thorax and tegula mottled cream and light brown, or rarely plain cream. Forewing length ♂, 9.2–11.4 mm, ♀, 9.1–10.0 mm; forewing ground colour predominantly cream, with some greyish mottling, particularly extensive in material from the Pyrenees; oblique fascia of raised black scales from basal part of costa to dorsum; three black dots of raised scales edged with ochreous in middle of forewing; two further spots before whitish subapical fascia; apical part greyish with black spots along termen; fringes grey. Hind wing grey-brown to moderately light grey, with some variation depending on substrate.

For those (like me) who find that too complicated and hard to understand I have pasted some images of males of the moth as shown in the paper.

I think this is a very nice gesture to honor Paul and the fact that without his vision, energy, and endurance DNA Barcoding would have never been such a success story. And what would be a better fit than naming a representative of the group he is most passionate about after him?

Wednesday, December 12, 2012

Barcoding CSI: The Hammer

I admit this is a very lurid title but indeed DNA Barcoding already founds its way into criminal forensics. Here the evidence:

(1) Fictional TV shows start using it to track down the bad guys. Yesterday in NCIS they used DNA Barcoding to convict somebody of albacore (Thunnus alalunga) smuggling. Ok, that's probably too far fetched but I have a better one.
Photo of the suspected weapon
(2) Earlier this year our lab helped with an investigation aimed to provide species identification on subsamples taken from a hammer for the OntarioSociety for the Prevention of Cruelty to Animals (OSPCA) and Toronto Police Service. Somebody was suspected to have killed a dog with a hammer. Hair and blood samples could perhaps confirm that the hammer owned by the suspect was the weapon.

Close-up showing a hair that was used to retrieve DNA
The lab was able to retrieve several short length sequences still long enough to be reliably matched to reference sequences of the domestic dog, Canis lupus familiaris. They were also able to retrieve some human DNA from the handle (not surprisingly) which could have been used for a STR profile.

However, that wasn't even necessary as the suspect confessed when confronted with the initial evidence provided by DNA Barcoding. 

Case closed. 

h/t Bradley Zlotnick and Chris Weland 

Friday, December 7, 2012

DNA photos

TEM image with intensity profile of λ-DNA fibers.
With all the hassle about endangered shark species in fin samples and continuous mislabelling of fish products I almost forgot to share what I thought are the pictures of the week.

Researchers from Italy were able to do direct imaging of double stranded λ-DNA in the A conformation, obtained by combining a novel sample preparation method based on a super hydrophobic DNA molecule self-aggregation process with transmission electron microscopy (TEM). A-conformation DNA is thought to be one of three biologically active double helical structures along with the conformations B and Z. It is a right-handed double helix fairly similar to the more common and well-known B form, but with a shorter more compact helical structure. 

A-DNAs superstructures used for image simulations
This is the first time that humans have captured direct photos of DNA. At present, the method only works with superstructures of DNA made up of six molecules wrapped around an seventh acting as a core. That's because the electron energies are high enough to break up a single DNA molecule. However, according to the researchers the problem could likely be solved by using a lower-power electron scope. With this technique, researchers should be able to see how single molecules of DNA interact with other biomolecules.

How cool is that?

Thursday, December 6, 2012

Still fishy

I have to admit it is going to be a fishy week on this blog but what can I do. After all one chooses what's close to ones heart ;-)

When it comes to DNA Barcoding in the media the really big stories had to do with fish or more precisely the seafood market. That started with the famous 'Sushigate' where two high school students used the method to show that many items on menus in seafood restaurants were simply mislabeled.

Frozen Tilapia - unfortunately often sold as red snapper
Quite a few broadcasters and newspapers took the idea and conducted their own investigations. Among those the Boston Globe. A year ago they tested seafood from Boston and with our help they found out that about half the time fish bought at restaurants across the region was mislabeled. They concluded:

Massachusetts consumers routinely, and unwittingly, overpay for less desirable, sometimes undesirable, species - or buy seafood that is simply not what it is advertised to be. In many cases, the fish was caught thousands of miles away and frozen, not reeled in by local fishermen, as the menu claimed. It may be perfectly palatable - just not what the customer ordered. But sometimes mislabeled seafood can cause allergic reactions, violate dietary restrictions, or contain chemicals banned in the United States.

Now a year later they went back to the restaurants and retailers to see if things have changed. Aparently they haven't:

Over the past several months, the Globe collected 76 seafood samples from 58 of the restaurants and markets that sold mislabeled fish last year. DNA testing on those samples found 76 percent of them weren’t what was advertised. Some restaurant operators who repeatedly mislabeled fish blamed suppliers. Others said naming inconsistencies were the result of clerical errors. Several made only partial revisions to their menus.

The main problem is that legislation hasn't caught up on the problem. Restaurants and suppliers know they will not face punishment for mislabeling fish. The Food and Drug Administration, which maintains a list of acceptable market names for fish species, has historically focused efforts on food safety, rather than economic fraud such as seafood substitution. However, they have already implemented DNA Barcoding as tool for seafood identification. Only regulation of the nation's seafood trade has to catch up which of course is a long and bureaucratic process. 

Most other nations are not even at this point yet.

Wednesday, December 5, 2012

Shark fins in BC

Shark finning continues to be a hot topic in Canada.

Just last week a bylaw banning the possession, sale and consumption of shark fins in Toronto had been  struck down by the Ontario Superior Court of Justice because it was supposedly outside the powers of the city.

Graphic by Vancouver Animal Defense League
Yesterday night a news report from Vancouver shows that fins of threatened and endangered shark species are being sold in Vancouver. Dried fins were purchased at local shops earlier this summer, some by an undercover reporter working for CTV and others by the Vancouver Animal Defense League, and sent to me here in Guelph for DNA Barcoding.

I had been in touch with the Vancouver Animal Defense League for a while already as a result of a blog post back in August in which I reported about efforts to ban shark fins from Canadian cites and provinces. What was lacking in all discussions and news releases was a clearer picture of what species are actually sold in Canadian shops. Earlier investigations in US restaurants had given us an idea but the actual extend was unknown. When I received the fins I was pretty sure that some of them were from endangered or at least threatened species according to the IUCN Red List but I was very surprised to find out that 76% of all samples sequenced fell into those categories. This was far worse than I thought and demonstrates how dramatic the situation is. 

If you want to get an impression of the dimension of the problem just go in one of the shops that sell fins as food or health products (if you happen to live close by). Have a look at the shelf's that are jam packed with dried fins and imagine that 3/4 of them are likely from species that are at least threatened. Now think of how many such shops there are.

Yesterday our results officially went public. I know that advocates of a province-wide ban of shark fin products in British Columbia are very positive as our findings will help them to substantiate their claims . 

Still - Very bad news for the sharks.

Tuesday, December 4, 2012

Number 2 is out!

Just finished working on the second one. The field is very productive and creative.

Have a click if you are interested. All citations in this pdf are hyperlinked. A simple mouse click will bring you to the article page on the publishers website.

Google Impact Award goes to CBOL

Today Google launched their Global Impact Awards to support organizations using technology and innovative approaches to tackle some of the toughest human challenges. From real-time sensors that monitor clean water to DNA barcoding that stops wildlife trafficking, the first round of awards provides $23 million to seven organizations changing the world.

Among them is the Consortium for the Barcode of Life (CBOL) at the Smithsonian Institution that will use its $3 million Impact Awards grant to create and begin implementing DNA Barcoding as an actionable tool for protecting the world’s most endangered wildlife. Working with researchers in six developing countries, CBOL will build a public library of DNA barcodes that law enforcement officials can use to identify confiscated material. The library is supposed to comprise approximately 2,000 endangered species and 8,000 species that are closely related to them or are commonly confused with them. The reference library will be part of GenBank.

Well, first of all, congratulations to CBOL for acquiring this grant. This is a great accomplishment especially in times where funding for biodiversity science is not on top of the list. The greater the news that the money is dedicated to advance the protection of endangered species.

Of course short press releases leave the interested reader with a lot of open questions and I have quite a few but I am sure there will be enough time for a closer look as soon as the project is up and running.

Monday, December 3, 2012

Water fleas in Middle Earth

Daphnia 'pulex'
Daphnia are one of the several small aquatic crustaceans commonly called water fleas because of their erratic swimming style. They live in various aquatic environments ranging from acidic swamps to freshwater lakes.

The identification of Daphnia species is difficult particularly in the so-called Daphnia pulex species complex . Determination of species based on morphological methods is only possible in a small number of species. Most others lack reliable morphological traits as a result of morphological stasis combined with a poor taxonomy. Initially the Daphnia pulex complex was considered to comprise of a few species but in recent years a number of new species have been identified genetically. Furthermore, each of these taxa comprises separate species in North America and Europe, despite carrying the same names.

There seems to be no alternative to a DNA Barcoding approach although there is an additional complicating factor, because similar to several other Daphnia species, North American Daphnia pulex members are able to form viable hybrid populations with Daphnia pulicaria. Any analytics should therefore include an allozyme analysis to confidently determine species status

Researchers from New Zealand have now used DNA Barcoding to identify invasive Daphnia specimens occurring in New Zealand lakes. They were able to document the establishment of non-indigenous North American Daphnia pulex members on the South Island. Cellulose allozyme electrophoresis was used to confirm that individuals were not hybrids with Daphnia pulicaria

New Zealand has only one recognized native Daphnia species, the relatively uncommon Daphnia carinata. These first confirmed recordings of members of the Daphnia pulex complex in New Zealand come from South Island lakes that are popular for overseas recreational fishers, indicating a possible means of  introduction in association with fishing and boating equipment.

The question is if this recent invasion will have any perhaps detrimental effect on the local fauna and flora. The authors think that the establishment of non-indigenous Daphnia might have large effects on lake and pond biota by probably reducing the abundances of both phytoplankton and other zooplankton (particularly rotifers). 

Who knows - lets hope that there might be ways to not find this out.

Friday, November 30, 2012

Nematodes and genetically-modified crops

Once in a while one comes across applications of DNA Barcoding you would never thought of in the first place although they perfectly make sense. It is nice to see that so many creative researchers are picking up the method and using it for questions they are interested in.

This post looks at the potential of DNA Barcoding for ecological risk assessment of genetically-modified crops. Dutch researchers from the National Institute for Public Health and the Environment were interested in crop induced changes in nematode assemblages in agricultural soils. Nematodes constitute a very diverse group within the soil fauna, feeding on microbes, invertebrates (including other nematodes) and plant roots. Such an intimate feeding relationship with all major players in agro-ecosystems implies that any effect genetically modified crop might have will likely be reflected in the nematode community. Better knowledge of nematode assemblage compositions could be used to extrapolate impacts on soil systems.

Nematodes in a sample
The classical methods to characterize nematode communities is based on morphological identification using light microscopy. However, this method is both very time consuming (on average several hours for 150 individuals per sample) and the resolution depends on the level of taxonomic expertise. For me they are all white to translucent small inconspicuous worms.

The overall goal of the study was to implement DNA Barcoding into a long-term monitoring network for soil impact of pest management products and the use of genetically-modified crops. Three parts are supposed to serve as baseline for future application. A first part represents the control and looks at seasonal fluctuations of nematode communities as a measure for natural variability over time. The second part focuses on the effects of current pest management (bio-fumigation using Brassica juncea) on nematodes, while the last part investigates the effects of genetically-modified crops (pathogen-resistant potatoes and amylase-potatoes) on soil nematode community structure.

The DNA-based approach to identification allowed for the analysis of nematode communities without microscopic pre-selection because it was based on a considerably broad (2,400 taxa) genetic database that covers the majority of terrestrial and freshwater nematode taxa. For the Dutch researchers one of the main advantages of using molecular methods is the time saving aspect as it allows for more intense and frequent sampling schedules.

Thursday, November 29, 2012

A whitefly puzzle solved

Bemisia tabaci or maybe not
The silverleaf whitefly (Bemisia tabaci, which is also referred to as Silverleaf whitefly strain B) is one of several whiteflies that are currently important agricultural pests.Their nymphs use parts of their mouth to stab into the plant and consume the plant’s juices. The honeydew they leave behind can induce the growth of sooty molds, which can then reduce the plants ability to absorb light. This results in less growth, lower yield, and poor quality plants.It is thought that the United States alone has suffered crop and ornamental plant damages in excess of $1 billion through this pest.

For 100 years, outbreaks were sporadic and relatively small, but this changed in the mid-1980s with widespread outbreaks occurring across the south western USA. This was odd because the whitefly was well known across the region as a minor pest yet here it was destroying large amounts of crops.  Although there were no morphological differences, molecular and biological data indicated that the outbreak pest was a different species. Using this information, it was proposed that rather than one species, Bemisia tabaci was composed of at least 28 different morphologically indistinguishable species, all separated by at least 3.5% divergence in their DNA Barcode. To date 34 species have been delimited using the same metrics.

These findings are supported by mating compatibility studies. These have shown that crosses between individuals identified as different cryptic species are reproductively isolated to the point that in most cases copulation does not occur and where it does, the resulting progeny are either sterile or reproductively inferior to their parents.

There was only one question left: Who is the the real Bemisia tabaci originally described in 1889?

A group of researchers has now solved this mystery. They were able to sequence a 496 bp DNA Barcode fragment belonging to a single whitefly taken from the original 1889 collection by Panayiotis Gennadius who first described the species. He had travelled to Greece to identify a small fly-like pest that was devastating tobacco crops there. It is clear now that it wasn't this species that invaded the US but rather a species that was provisionally called "Mediterranean". This species has now begun its own global journey of invasion spreading from its Mediterranean home range to at least 10 different countries in Europe.

Wednesday, November 28, 2012

Bigfoot does not exist!

It is a myth as much as the yeti, the unicorn, mermaids, giant octopus that attack ships and drag them to the bottom of the ocean, the Bermuda triangle, aliens at area 51, little green aliens on Mars, Santa Claus (sorry kids), the Easter bunny and so on. I could probably fill the entire blog post with mystical creatures and suspicious encounters of similar credibility. 

Why would I do that? Because some really bad science is making the headlines again.

A dubious scientist claims to have sequenced Bigfoot DNA. Dr. Melba Ketchum from Nacogdoches (her company) claims:
Our study has sequenced 20 whole mitochondrial genomes and utilized next generation sequencing to obtain 3 whole nuclear genomes from purported Sasquatch samples. The genome sequencing shows that Sasquatch mtDNA is identical to modern Homo sapiens, but Sasquatch nuDNA is a novel, unknown hominin related to Homo sapiens and other primate species. Our data indicate that the North American Sasquatch is a hybrid species, the result of males of an unknown hominin species crossing with female Homo sapiens."

First and foremost, these results are nowhere published and Ketchum is not sharing them not even more details on the methods used. No reputable scientist makes a press release before a paper has been published. If true any big journal would take the story and insist on doing the PR using their own machinery. Obviously this didn't happen which makes these 'results' not more reliable than any of the shaky videos, blurry images or dubious witness accounts that are called evidence for the existence of Bigfoot.

Good science is shared with the scientific community to allow colleagues a critical view at results and the conclusions. Currently we are left with a pretty much meaningless press release

Dr. Ketchum, if you want anyone to believe your findings release them! Until that happens I and hopefully anybody else with some common sense sees Bigfoot as just another hoax. Unfortunately, these 'news' are currently all over the place and many outlets take the outrageous claim for granted. Bye bye critical thinking. Dear press - you shouldn't buy everything just because it says DNA on the label. The fact that these researchers claim they used DNA analyses doesn't mean a thing. The new hominid nuclear DNA might as well be chimeric and the human mtDNA from a researcher that sneezed on the samples. Most importantly, where did the samples come from? I hardly dare ask, but is there a voucher specimen?

That leaves us with two unproven claims. (1) There is such a being like Bigfoot, and (2) the hybrid between an unknown hominid and a human was actually fertile and evolved into a species that survived the last 15,000 years in North America.

I don't buy it!

Tuesday, November 27, 2012


When I recently did my little number crunching exercise I was also looking at the percentage of DNA Barcoding papers that have been published in open access journals. Among the major ones was of course PLoSONE but there were also a few others that have papers available without subscription fees. However, it only amounts to a total of 12% of the publications that are available to everyone. In turn that means that about 88% of all DNA Barcoding papers are not available to every researcher on the planet. I find that very frustrating as I thought that especially in this new field there is more inclusiveness!

In 2006 Marguerite Holloway published an article in Conservation in Practice in which she tried to capture the innovative thinking behind the at that time very new method called DNA Barcoding. The title was "Democratizing Taxonomy" referring to Dan Janzen and Winnie Hallwachs who believe passionately that greater access to knowledge and technology will transform the future of conservation. I've heard this term from Dan in various of his talks and I am always reminded of it when it comes to publishing as researchers do not live in a free publishing world. This is especially true for all of us in early phases of our careers where an insufficient measure (impact factor) is dictating where to publish. The result is that many researchers, maybe even the majority, have no access to a lot of what we've published over the last 10 years just because they or their institution can't afford the often ridiculously high subscription fees. That's a shame!

The more happy I am to announce the birth of a new journal with a new business model of open access publishing. PeerJ is a new multidisciplinary open access journal that announced today the first formal call for papers. Unique among academic publishers, PeerJ provides authors with low cost lifetime memberships giving them the rights to publish their papers freely thereafter. A basic membership plan is only $99 that would give an author the right to publish once a year for the rest of their life. That seems reasonable and compared to some of the usual fees of other open access journals it is very cheap. Access to the articles is of course free!

Friday, November 23, 2012

Agarwood barcoding

Aquilaria crassna
Aquilaria crassna is a tree species that has been of great ethnobotanical importance to people throughout the Greater Mekong region and beyond. Its heartwood and resin are highly valued commodities that have been transported along long-established trade routes for thousands of years. However, this species has now become Critically Endangered, owing to over-exploitation.

The wood from Aquilaria crassna (Agarwood) contains aromatic resin, known as ‘gaharu’. This is produced by the tree in response to injury if the production of callus tissue is inhibited. It acts as a chemical barrier to attack by insects and fungi. However, under natural conditions gaharu is not produced by trees at all. This resin is often used in temples as perfume wood. The wood can also be distilled to yield a valuable essential oil, which is widely used in Chinese and Southern Asian medicine and also in the Middle East for making perfumes and cosmetics. 

Currently the majority of the wood comes from wild populations and there is now a very real danger this species may become extinct if wild harvesting continues at the current rate. To conserve this species, it is vital that this plant becomes more widely grown in cultivation, to reduce the pressure on the few wild populations that remain. Cultivation requires high quality seed and especially in Vietnam there is concern that a range of hybrid species or other members of the genus could lead to production loss and disappearance of the original species. Proper species identification starts with the seeds used and Vietnamese researchers have now tested if DNA Barcoding could help. Not surprisingly it worked quite well and one of the official plant markers, rbcL along with ITS was tested most effective.

Probably it needs to reemphasized that DNA Barcoding cannot identify hybrids (oh well, I probably should say mostly, but that's a different story...) but it can help to distinguish between seeds of different Aquilaria species obtained in the wild and destined to be used in cultivation.

Thursday, November 22, 2012

Helpful weevils

Eurasian milfoil (Myriophyllum spicatum)
Eurasian milfoil (Myriophyllum spicatum), a submerged aquatic plant that grows in still or slow-moving water, is one of the worst aquatic plant pests in North America. Like native aquatic milfoils, it has feather-like underwater leaves and emergent flower spikes. Usually leaf shape and size can be used to distinguish it from other milfoil species. However, Eurasian milfoil is a variable species, often making it difficult to identify without chemical or DNA analysis. It has been known to crowd out native plants and create dense mats that interfere with recreational activity. Eurasian milfoil can grow from broken off stems which increases the rate in which the plant can spread and grow. 

One of the many lakes that are heavily invested with this invasive plant is Christina Lake in British Columbia, Canada. In the lake milfoil is currently controlled by having dive teams who manually extract the plant from June until October. Those teams work seven days a week with one overlapping day just to keep the nasty aquatic weed at bay. 

Milfoil weevil (Euhrychiopsis lecontei)
Obviously it would be much easier and cost-effective to develop biological pest control strategies and there are a few species that have been discussed and used. The water veneer moth (Acentria ephemerella), feeds upon and damages this water milfoil. It has been used as biocontrol but carefully, as it lacks host specificity and attacks other plant species, including natives. In addition it is also an introduced species. Another method for biocontrol is grass carp, (Ctenopharyngodon idella), is sometimes released into affected areas, since these fish primarily feed on aquatic plants and have proven effective at controlling the spread. However, the carp prefers native species before turning against Eurasian milfoil and more imporantly it has become a serious pest in North American lakes as well. That leaves us with the milfoil weevil (Euhrychiopsis lecontei), a native species that specifically loves to eat the new growth on the pest thereby stunting the plant’s growth and propagation.  that a weevil that lives in the region is actually this native species, making it possible to rear and release more of the bug. In the case of Christina Lake it needed DNA tests to confirm that the right kind of weevil naturally occurs in the lake. This makes it possible to rear and release more of the bug as it will be easier to get permission to introduce more of them to help control the ever growing milfoil. Regional authorities now hope that a pilot project can be started as early as coming summer. Eventually they would like to see a business created that will raise weevils to release not only into Christina Lake, but other lakes around the province to naturally control the alien species of Eurasian Milfoil.

Wednesday, November 21, 2012

Barcoding types

When describing a new species, taxonomists provide us with a species name and designate a type specimen to which this name will be permanently attached. In other words, a type is an example that serves to anchor the defining features of a particular taxon. 

DNA Barcodes can be used both to attribute species names to a given specimen and to flag genetic clusters for which no name is available. In an ideal situation this can be achieved by sequencing type specimens. However, the majority of the type specimens that are in our Natural History Museums is fairly old and not necessarily stored under DNA-friendly conditions. Many are conserved in formalin which destroys DNA over time. Others, like many insects, are pinned and boxed. From time to time researchers were able to extract DNA from such specimens but mostly they focused on considerably younger specimens (collected and described more recently) or addressed a very small number of samples as it is a more  laborious process.

Eois isographata (credit
In a new study researchers from Austria and Germany report successful sequencing of DNA Barcodes from 96 historical specimens (92 type specimens +4 non-types) of the moth genus Eois (in the 79 to 157 year age range). They used six primer combinations (recovering between 109 and 130 bp each) to assemble a full-length barcode sequence for each specimen. And indeed they were able to generate sequences with an average length of ~500 bp. Furthermore, they developed a non-destructive DNA extraction which means that the often very valuable type is not destroyed in the sense that no additional damage compared to conventional preparation of genitalia slides is inflicted on the specimen. Genitalia slides are usually necessary for morphology-based identification and description. This is still possible after the extraction procedure.

What strikes me is the fact that they were still able to retrieve enough DNA to apply the primer sets they had designed to come up with DNA Barcodes of reasonable length albeit they had to admit that the work is considerably more expensive than 'regular' DNA Barcoding. Nevertheless, a big step forward to anchor another defining feature to some types. Only this time it is one far more objective than many morphological characters out there.

Tuesday, November 20, 2012

Oak killer

The goldspotted oak borer, Agrilus auroguttatus, is a woodboring beetle best known for destroying stands of oak trees in San Diego County, California, in the United States. This pest is native to southeastern Arizona, although a related species occurs in southern Mexico and northern Guatemala. Little is known about the life history of the insect, whether it is introduced or moving into the area as part of a natural range expansion, nor do we know anything about its current distribution. What is even more puzzling is the fact that it has never been known to cause the kind of oak destruction as it was observed in California. As of 2010, Agrilus auroguttatus has killed an estimated 21,500 trees covering 1,893 square miles in San Diego County but some estimates put the numbers at 80,000 trees.

So far the problem was restricted to San Diegio County but now the species was found 65 km north in Riverside County which is very alarming for local authorities. Larvae extracted from under the bark of a recently-killed California black oak were subjected to DNA analysis at the University of California Riverside and confirmed to be Agrilus auroguttatus

As for the one discovered in Riverside County it is believed to have made the jump from San Diego through the movement of infested firewood. It is my hope that this was an isolated find and the early discovery helps to stop it from spreading further North. Its close relatives, the emerald ash (Agrilus planipennis) and bronze birch borer (Agrilus anxius) have caused more than enough havoc among North American trees. This species now poses a major threat to susceptible oak species throughout California, southern Oregon, and beyond. Currently there are no effective tools for protecting trees once infestation occurs.

Monday, November 19, 2012

Midden barcoding

For most of us midden is an expression for an old dump for domestic waste. Archaeologists use it to describe any kind of feature containing waste products relating to everyday human life. 

In the animal kingdom, ground burrows are also known as middens although they are primarily used for food storage. A midden may also be a regularly used toilet area or dunghill, created by many mammals, such as the hyrax, and also serving as a territorial marker..

In the case of some 30 000 year old American and Australian middens, the animals urinated and defecated on their nests during the course of habitation, and organic material such as plant and animal tissue, bone, hair and eggshell gathered from the local surroundings, became cemented together into a hard, impermeable mixture.

With the advent of affordable and accessible high-throughput sequencing and methods to extract ancient DNA it is now possible to genetically screen a wide range of complex modern and ancient substrates, with an unprecedented depth of sequence coverage. Recently studies have attempted the isolation of DNA from samples – including fossil rodent middens – collected in cool and dry environments but so far not from hot and dry regions. Cool and frozen environments were considered more suitable to long-term DNA preservation. However, an international team of researchers has now managed to isolate DNA from 30 000 year old faeces matter to ascertain which plants and animals existed at that time in a couple of hot and dry regions in Australia and South Africa. 

Using several genetic markers and next generation sequencing they discovered a range of plant and animals, some of which are now locally extinct, such as the common brushtail possum found in one midden in the Cavenagh Range in Western Australia. The group found flora and fauna that had previously gone undetected in different types of studies, such as a range of previously indistinguishable dry zone grasses.

Friday, November 16, 2012


Imagine a course where students learn about a country’s delicate ecosystem by exploring the various geographical zones, their inhabitants and the challenges they face. The key to creating an authentic experience rather than providing typical student “destination” travel is meeting with local guides, many of whom are naturalists possessing an intimate knowledge of the ecology and culture of a country or region. Students get acquainted with these so called visionary collaborators, providing them with an opportunity to be inspired by their work. In Costa Rica student groups have the chance to work with the renowned ecologist Dan Janzen and his team, whose conservation field the Area de Conservacion de Guanacaste (ACG) includes more than 325,000 species. Ultimate goal is to generate a DNA Barcode for each one.

The two former teachers Crawford Hill and Eddie Rodriguez are running Chill Expeditions a company that offers teenage students an adrenal rush on their trips, such as whitewater rafting, climbing active volcano peaks and zip-lining hundreds of feet above a rain forest to take in a “monkey’s-eye” view of the jungle canopy. But they are quick to point out the emphasis is just as much an in-your-face cerebral experience as described above. They call this unique experience eco-immersion. To further deepen their interaction with the local communities, the students take part in service projects when available. Hill said, for instance, that about two dozen student groups from all over America recently participated in building a school in Costa Rica over a period of a year. Students have also helped local indigenous people to build and install clean-burning stoves, which use less wood and produce less smoke, replacing those that have caused respiratory illness in their villages. Other projects have included planting organic gardens, laying sidewalks and using recycled materials to build walls.

A great hands-on experience on how ecology impacts a country and its people and a wonderful way to introduce teenagers to an entirely different world.

Thursday, November 15, 2012

Lonesome George’s kin

Lonesome George (Source: BBC)
In June 2012 the presumably last individual of the Pinta Island Giant Tortoise species (Chelonoidis abingdonii) died at about 100 years of age at the Charles Darwin Research Station on the Galapagos. Its name was Lonesome George, and over the years it had become famous as the rarest creature in the world. George served as a potent symbol for conservation efforts in the Galápagos and internationally.

Over the years all attempts at mating Lonesome George with other closely related species had been unsuccessful. Therefore, everybody mourned the extinction of this tortoise subspecies in this summer.

And today the potentially good news: On the remote northern tip of Isabella Island, a group of researchers of Yale University collected DNA from more than 1,600 tortoises and discovered by comparison with DNA from museum specimens that 17 of them were ancestors of Chelonoidis abingdoni, native to Pinta Island of which Lonesome George was the last known survivor. The 17 tortoises are hybrids, but evidence suggested a few might be the offspring of a purebred Chelonoidis abingdoni parent. Five of these tortoises are juveniles, which suggested to researchers that purebred individuals may still live on the rocky cliffs of Isabella in an area called Volcano Wolf.

The researchers and the Galapagos Conservancy now hope to collect the hybrids and any surviving purebred members and begin a captive breeding program that would restore this species.

The publication is unfortunately not accessible yet but I will update the link when Elsevier decides to release it. Did I mention that I think that all press releases should always be accompanied by full open access to the publication for everyone? Bloggers like me love these kind of news but we also want to read more than the digested version that goes to the press. Especially after the ENCODE disaster.

Wednesday, November 14, 2012

Numbers Part II

Here it is - episode two of me playing with numbers of publications on DNA Barcoding. If you recall I was looking at over 2000 publications of the last 10 years to provide some insight into the progress the discipline was making within such a short time. I was very happy to see that Mark Stoeckle has added to this look at the big picture by sharing some DNA Barcode stats from his treasure box. Next time you have to prepare a talk on DNA Barcoding and you need some convincing figures on progress and development over the last years feel free to 'steal' my graphs and I am sure Mark would be happy to see his material used as well. Just don't forget to tell everybody where you got it from :-)

When looking at the publication data I was also very interested on how DNA Barcoding has been incorporated into the more applied areas of science. Therefore, I grabbed 208 that were clearly representing studies of applied DNA Barcoding, and categorized them into four different groups I considered most interesting. The largest number of publications I was able to find in the field of pest research and management. The majority of those were focusing on crop damaging animals and ways to identify them. A lot of papers were also published on health related topics mostly the identification of disease vectors. Both conservation and forensics are dominated by studies that assess the value of DNA Barcoding for regulatory purposes but you can even find research on potential applications in criminal forensics. These numbers show that DNA Barcoding is not just an effort of a few 'stamp collectors' travelling around the globe in order to complete their little collection books but rather a still young discipline that has already been translated into applications that are directly beneficial to society.

My only other graphic today demonstrates how diverse the field has become as I was looking at the number of journals that actually had published DNA Barcoding papers and if there were actually some preferences among authors or even publishers. In total 157 different journals have published at least one DNA Barcoding paper. Most did more than that. Therefore, the first take home message is that DNA Barcoding is widely accepted and appeals to a variety of topic journals. Two journals are leading the pack and that's not a surprise as both have been trying to become home for DNA Barcoding research publications. Molecular Ecology Resources has a strong focus and PLoS ONE with its inclusive concept is catching up quickly.  The third place is another very good indicator how DNA Barcoding has impacted taxonomic research. Zootaxa is the world leading journal on taxonomy and main home for species descriptions and revisions. If they would just starting to use DOI's but that's another story for another post...

The good news is that researchers can actually choose where to publish depending on their needs and perhaps even strategically. DNA Barcoding is certainly not an exotic field anymore. This is also good news for anyone like me who prefers options that are open access even if it comes with the price of a lower impact factor.