Tuesday, October 30, 2012

Illegal Hunting

Pampas deer (Ozotoceros bezoarticus)
Illegal hunting is one of the major threats to vertebrate populations in tropical regions. This practice has serious consequences not only for the target populations, but also for the dynamics and structure of tropical ecosystems. Generally, in cases of suspected illegal hunting, the only evidence available is pieces of meat, skin or bone. In these cases, species identification can only be done by using molecular technologies.
Brazilian researchers have now used DNA Barcoding in three cases of suspected wildlife poaching. They were able to identify the species killed and solve ongoing criminal investigations. 

Capybara (Hydrochoerus hydrochaeris)
In July 2010, based on suspected illegal hunting, a wildlife inspector of the Brazilian Environmental Agency (IBAMA) seized and sent biltong samples of a mammal species to  Sao Paulo State University. According to the inspector, the suspect claimed that the meat was pork, but there was no evidence to confirm this assertion. It turned out to be Capybara (Hydrochoerus hydrochaeris). Along with this sample, the researchers received a second meat sample, which was removed from the wings of an unidentified bird species. This was identified as Chaco Chachalaca (Ortalis canicollis). In February 2011, they received a mammal meat sample taken by another IBAMA wildlife inspector. The seized meat was confiscated from a suspect’s freezer during routine surveillance activity and could be identified as Pampas deer (Ozotoceros bezoarticus). Hunting these animals is illegal in Brazil and and based on the results this study, the defendants were found guilty and punished with fines; they may still be sentenced to prison for a period of 6 to 12 months.

Chaco Chachalaca (Ortalis canicollis)
A wonderful example that molecular forensic techniques can provide an important tool that enables local law enforcement agencies to apprehend illegal poachers. 

Friday, October 26, 2012

Bluetongue disease

Blue-tongue infected sheep may also
bend their necks in a strange manner
(Photo: Onderstepoort Veterinary Institute)
Blue-tongue disease is a non-contagious, viral disease of ruminants, mainly sheep and less frequently cattle, goats, buffalo, deer, dromedaries and antelope. It is caused by the Bluetongue virus which is transmitted by the midge Culicoides imicola and other culicoids. Major signs are high fever, excessive salivation, swelling of face and tongue as well as cyanosis of the tongue. Swelling of the lips and tongue gives the tongue its typical blue appearance, though this sign is confined to a minority of the animals. Nasal symptoms may be prominent, with heavy discharges at times. The mortality rate is normally low, but it is high in susceptible breeds of sheep. In Africa, local breeds of sheep may show no mortality, but in imported breeds it may be up to 90 percent.

Culicoides obsoletus
Blue-tongue has expanded its range in recent decades, probably due to the expansion of its main vector and the presence of other competent vectors such as Culicoides obsoletus and Culicoides pulicaris both of which are spread widely throughout Europe. Consequently the disease has been travelling through Europe and many countries there are trying to be proactive with respect to the spread of the disease.

A good example is a new study from Spanish researchers that utilizes DNA Barcoding to map the distribution of biting midges and to understand their feeding patterns in areas susceptible to bluetongue. They confirmed the presence of the potential bluetongue vector Culicoides obsoletus on two of the islands in the Canary archipelago (Spain) and demonstrated the susceptibility of ruminants (goats and sheep) to the attacks of this biting midge species by analysing their bloodmeal. 

Given that Culicoides obsoletus has been shown to be one of the main vectors of this viral disease in continental Europe and given the high density of ruminants that are fed on by this midge species on these islands all necessary elements for an outbreak are given on the Canary Islands. It hasn't happen yet but it seems paramount to set up an active surveillance program on these remote islands as infected midges can drift all the way from Africa or continental Europe.

Open access publishing

I am a great supporter of open access publishing in science. It's great to see that more and more DNA Barcoding papers are published in open access journals, and I try to support this as much as possible e.g. by being an editor in PLoS ONE and encouraging colleagues and students to use such journals in favor of the traditional ones.

Yesterday, one of my favorite sites for fun and humor related to work  - PHD Comics released an animated cartoon explaining everything around open access publishing and why one would do it. The cartoon is build around phone interviews with two prominent advocates for open access publishing - Nick Shockey and Jonathan Eisen. 

I think it is a little masterpiece worth leaving your work aside for 8 1/2 minutes.

Thursday, October 25, 2012


Just found this:
DNA 11, the company that introduced the world to DNA Art, is taking it to the next level with DNA 11 Ancestry Portraits, where your genetic lineage is encoded to create a one-of-a-kind canvas art piece.

For $440 you can get your mtDNA haplotype encoded in a 2D barcode that is smartphone compatible and redirects everyone to a personalized website. They have a lot of interesting things at DNA11 - check it out.

How about a gel image on your living room wall? They also make carpets.

Wednesday, October 24, 2012

Why should high school students do DNA Barcoding?

Because it's fun!

You probably have figured out already that I am particular fond of the idea to involve citizens in actual science projects. Especially high school students could benefit from this quite a bit. Here just one example. 

The video is 2 years old but fun to watch anytime.

In case you have a high school teenager at home looking for a science fair project - why not suggesting DNA Barcoding  as a topic?

Malagasy endemics

Euphorbia pulcherrima
not necessarily endangered

One of the largest genera of flowering plants is Euphorbia with approximately 2,000 species. This large genus belongs to the very diverse Family Euphorbiaceae with at least 7,500 species. The variation within this genus is astonishing, from low-growing garden weeds called spurges to giant, cactus-like succulents that rival in size with North American sahuaro and organ-pipe cacti. The most famous member is most likely Euphorbia pulcherrima, better known as Poinsettia indigenous to Central America and widely used in Christmas displays all other the world.
Isotype of
Euphorbia mananarensis
Madagascar is the home of at least 170 native mostly endemic Euphorbia species. Nearly all of them are listed in the CITES Appendices I and II as they are threatened by habitat loss and illegal collection of wild plants. The absence of a reliable taxonomy makes it particularly difficult to identify these plants, even when fertile, and thereby compromises the application of CITES regulations that are in place to protect them. Many Malagasy species of Euphorbia are illegally collected in the wild by unscrupulous collectors and internationally traded, presenting significant threats as a result of overexploitation, sometimes leading to the total decimation of entire populations.

DNA barcoding can provide species-level identification irrespective of developmental stage and the presence of flowers or fruits and may be a promising tool for monitoring and controlling trade involving those threatened species. A group of researchers from France have now published a first study on 41 Malagasy Euphorbia species in which they successfully tested several markers including the ones proposed by the plant barcoding community. 

Currently, all succulent species of Euphorbia are covered under the CITES convention. Yet, it is not always possible to determine whether a plant, cutting, seed or other propagule belongs to a succulent species, and as a consequence, material of other species may erroneously be subjected to CITES control. Moreover, some succulent Euphorbia currently covered under CITES are in fact common and widespread, and international trade does not represent a threat, yet it is often impossible to distinguish them from other succulent species that are highly threatened. Reliable barcoding procedures for all Malagasy Euphorbia could help resolve these issues, enabling control for those species that require it while allowing trade for those that are not threatened, and thereby providing a much-needed source of sustainable income for Madagascar.

Tuesday, October 23, 2012

Gaga again

Graduate Student Fay-Wei Li at the moment he
discovered Gaga germanotta alive in Costa Rica.
Seems that quite a few taxonomists are fond of Lady Gaga's music. How else can one explain that her name has been used for a taxonomic description. A small parasitic wasp last time and now an entire fern genus found in Central and South America, Mexico, Arizona and Texas. As a result 19 species of ferns will carry the name Gaga. Two of the species in the Gaga genus are new to science: Gaga germanotta from Costa Rica is named to honor the family of the artist, who was born Stefani Germanotta. And a newly discovered Mexican species is being dubbed Gaga monstraparva (literally monster-little) in honor of Gaga's fans, whom she calls little monsters.

We wanted to name this genus for Lady Gaga because of her fervent defense of equality and individual expression, said study leader Kathleen Pryer from Duke University. Also in one of her performances Gaga wore a heart-shaped costume with giant shoulders that looked, according to Pryer, exactly like the bisexual reproductive stage of the ferns, called a gametophyte. It was even the right shade of light green. 

However, the clincher came when they scanned the DNA of the ferns (including the plant DNA Barcoding regions) being considered for the new genus. A quartet of base pairs characteristic for the genus spelled out GAGA. 

No matter if one likes her music or not. I give Lady Gaga a lot of credit for her Born This Way Foundation, a national anti-bullying initiative. 

Furthermore, I congratulate all those creative taxonomists for coming up with new names honoring celebrities (well maybe not always honoring). 

A new fighting fish

DNA Barcoding has often been criticized for not following through on new discoveries. There are a lot of studies that resulted in the discovery of potential cryptic species but many of these new entities have never been named and formally described. Many of them bear an interim taxonomic name or a number code which gets propagated quickly. One of the reasons for that might be that it takes an awful lot of time to go through the lengths of formal description by following the rules set by International Commission on Zoological Nomenclature

Frankly, for researchers in earlier stages of their career - and I consider myself one - it is also an intimidating thought to publish a description that is initially (and sometimes exclusively) based on molecular evidence knowing that there are some big names in your taxonomic field, full of resentment towards DNA Barcoding, eagerly waiting for a Barcoder showing a weak spot. I had the arguable pleasure of receiving some snarky comments in the past years and I haven't even started to formally describe some fish although I probably should.

Furthermore, a taxonomic description doesn't give you much credit which in turn could count for your career. Unfortunately, they way we measure success in science and assess candidates for academic positions relies heavily on impact factors and citation indices. This is an alarming development in general and a huge problem for taxonomy in particular. 

What are we supposed to do as researchers that don't have a tenured faculty position? We are to a considerable extend measured based on our publications and their impact. It might sound harsh but it is true - a description of a new species or a revision of a genus doesn't help you to position an article in a high ranked journal, and that's what many search committees are looking for to find the best candidates in a big pile of applications.

So, I am not surprised that so many potential species discovered by DNA Barcoding haven't got a name yet, and I haven't even talked about the fact that the rate of discovery is simply becoming to high for traditional taxonomic culture to catch up. That's why it is important to showcase examples where things are falling into place although it might take a few years before it happens.

Betta mahachaiensis (from article)
The fighting fish genus Betta is a good example for a group where we haven't be able to worm out all secrets yet. In 2010 a DNA Barcoding study contributed new (molecular) evidence to the case for a new species and furthermore indicated two more overlooked species in the genus Betta. Two years later the confirmed species was formally described as Betta mahachaiensis and further descriptions were announced therein. These beautiful little fish belong to a group of Betta that build bubble nests, floating masses of bubbles blown with an oral secretion or saliva that will eventually host their eggs. Males will build those nests of various sizes and thicknesses, depending on the male's territory and personality. Some males build constantly, some occasionally, some when introduced to a female and some do not even begin until after spawning. Fishes of this new species have been found with their nests in the phytotelma of a palm. The molecular findings are one part of the entire story. There are also morphological traits characteristic for the new species.

Nipa palms with B. mahachaiensis in their phytotelma
The message for those critiques that say DNA Barcoding research leaves behind a lot of unfinished business is that we do what we can to follow currently accepted practice. However, as I tried to made clear in my introduction to this post there are quite a few factors making this extremely difficult, especially for young academics, and it requires the entire community to resolve the real issues behind that. Offending comments and destructive reviews bashing DNA Barcoding are not helpful at all and hopefully a relict of the past.

Monday, October 22, 2012

Enemy of wine

The Grape is perhaps the most economically important crop in Chile, with vineyards covering over 180,000 hectares in 2007, and about a third of production dedicated to table grapes. This crop accounts for about 42% of all fruit exports in Chile. The country is also the fifth largest exporter of wines in the world, and the ninth largest producer.

Mealybugs (Pseudococcidae) is the common name for some among the most destructive plant pests. They are scale insects coated with a powdery mealy waxy secretion; that feed on plant juices. Mealybugs are considered pests on many plants, including apple, avocado, cassava, citrus, coffee, grapes, pineapple, rice and sugarcane. The main phytosanitary problem for international sales of Chilean table grapes are mealybugs, e.g. 71.5% of all table grape rejections during inspections before export have been attributed to these tiny scale insects. They also deposit honeydew on the fruit, on which sooty mold subsequently develops
Correct identification is essential when dealing with species considered as pests. Insecticide applications have to be timed properly because different species occupying the same host may have different biological characteristics. Furthermore, natural enemies of mealybugs tend to specialize on particular species.  Therefore, any biological control program relies on proper identification of the mealybugs present. Another problem is that in international trade, different markets identify different mealybug species as quarantine pests. However, scale insects are not so easy to identify and mealybugs comprise over 2000 species!

Chilean researchers have now used DNA Barcoding to identify the most common mealybug species in their country thereby establishing a DNA library that will help for future inspections and studies. They could show that  Pseudococcus viburni, Pseudococcus meridionalis and Pseudococcus cribata are the main pest species of grapes in Chile's main grape production area. The genetic variability of Pseudococcus viburni and Pseudococcus cribata, at two molecular markers used (COI and ITS), suggest that they are either native or long-established in the region. In contrast, no genetic variability was found in Pseudococcus meridionalis, suggesting that this species may have been recently introduced to Chile.

This was already the second study on these pest species and given their importance for fruit production it certainly won't be the last one. Another group had looked at the potential of DNA Barcoding for species in France and Egypt.

Friday, October 19, 2012

Dangerous snails

Nassarius papillosus
Nassa mud snails (genus Nassarius) are small sea snails that are very active scavengers, feeding on crabs and carrion such as dead fish. They often burrow into marine substrates and then wait with only their siphon protruding, until they smell nearby food. As scavengers, they help maintaining the ecological balance of their benthic community.

They are also useful for biomonitoring of Tributyltin (TBT) in marine environments. Due to a high specificity and sensitivity to TBT, imposex is found in some Nassarius species. Imposex is a toxin-caused pathological condition were snails develop sex organs that are in contrast to their actual sex. Imposex levels are considered the best biological indicator of TBT pollution in aquatic environments.

Even more importantly, there is a serious food safety problem involving these snails. There is a range of species occurring at China's coasts and most local Nassarius species are consumed as food. Due to the life style of the snail, a variety of toxins (e.g. tetrodotoxin) can be accumulated in their body and pose a threat to consumers. In the last couple of years several food poisoning incidents caused by Nassarius have been reported in China. In some cases victims died of the poisoning. This led to a regional ban that prohibits the sale and consumption of Nassarius.

Recent studies showed that the toxicity of Nassarius is species specific. For example, N. hepaticus is considered toxic while N. festiva isn't. In another species (N. succinctus) the toxicity changes seasonally.

A group of researchers from the Ocean University of China, Qingdao have now tested the utility of DNA Barcoding to help with species identification as it is not as straightforward as needed for food safety monitoring. Their results are very promising as they were able to show that DNA Barcoding is capable to distinguish between species. Furthermore, they found several cryptic species candidates and more concerning high levels of phenotypic plasticity in one species.

Thursday, October 18, 2012

Real Feta

According to the relevant European Union legislation, only those cheeses produced in a traditional way in some areas of Greece (mainland and the island of Lesbos), and made from sheep milk, or from a mixture of sheep and goats’ milk (up to 30%) of the same area, may bear the name "feta". Everything else should be called white cheese although similarly brined cheese products are found elsewhere in the Mediterranean region.

Similar brined white cheeses produced outside the EU are often made partly or wholly of cow's milk, and they are sometimes called feta. Not a legal problem if they are sold outside the EU, e.g. here in Canada, but inside it is illegal. 

I admit I am one of those people that prefer the real feta or at least the one made from sheep milk. In Canada it is hard to get and if you do it costs a fortune (as most quality cheese). Instead you mostly get a cow milk alternative. This is not a big problem but if you are in the motherland of feta and you buy a product labelled "feta" you can expect the real stuff. 

Well, researchers from the Institute of Agrobiotechnology at the National Center for Research and Technology Hellas (CERTH) in Thessaloniki showed that this isn't necessarily true. They used DNA Barcoding and were able to show that some products were mislabeled as they contained cow's milk, sometimes mixed with goat milk, but no sheep milk. 

They also tested other products sold in Greece and developed markers to be able to identify local varieties of cherries, lentils and beans. On average they found 20% of the samples being wrongly labelled. Cheaper alternatives are sold as the more expensive product. Another product tested was basmati rice which in up to 50% of the cases turned out to contain Greek varieties of non-aromatic rice that are much cheaper.

As a consumer my first reaction to such findings is always anger although my experience tells me to expect this. However, news like this also raise the hope that matters will change as we do have the tools in place to find out the truth. We just need to apply them more often.

Wednesday, October 17, 2012

Biology for geeks

Last month I had posted about options to include citizen scientists in our field work efforts. Even more exciting is the ability to give every citizen the means to participate in the research effort. One great example is Foldit, a computer game enabling everybody to contribute to important scientific research by simply playing it. Researchers are thereby collecting data to find out if humans' pattern-recognition and puzzle-solving abilities make them more efficient than existing computer programs at protein pattern-folding tasks. If this turns out to be true, human strategies can be taught to computers to make protein folding algorithms faster and more efficient.

In 2008 Mackenzie Cowell and Jason Bobe created DIYbio.org an organization dedicated to making biology an accessible pursuit for citizen scientists, amateur biologists and biology professionals. In so-called "biohacklabs", such as Genspace, amateur biologists can come together to create projects, whether just for fun, but also to improve their knowledge or engage in existing projects contributing to current research efforts.

The DIYbio network currently consists of 29 groups from 14 countries. One of those is LaPaillasse, led by Thomas Landrain, a PhD student in Synthetic Biology. The first french community lab for biotech is a real lab connected to /tmp/lab, a hacker space in Vitry sur Seine for people doing creative things with technology, culture and arts as an online community. The goal is to get together people from the most varied horizons, making projects together and sparking new ideas for the 21st century. Various people are developing new ideas, new projects, new arts, bridging the digital divide, helping people to grasp technology in a creative manner, communicating our open vision of the world, empowering people to develop their project with new technologies..

One of the projects is DNA Barcoding and the La Paillasse started with a couple of workshops to introduce the idea and the methods involved to interested participants.

Saturday, October 13, 2012

Bats help with pest control

Tadarida brasiliensis (Credit  Merlin D. Tuttle)
Many bat species are known to be friends to agriculture, their diet helps reduce the need for pesticides, they are important pollinators, and their guano is an effective fertilizer. The Brazilian Free-Tailed Bat (Tadarida brasiliensis) is no exception to this.

But there is more to this - a new study in PLoS ONE shows that the bats are tracking abundance of their prey in space and time. 
By using a qPCR fecal DNA assay (using COII probes and as confirmation of species ID COI Barcodes), scientists were able to show a significant association between the numbers of Tadarida brasiliensis feeding on corn earworm moths (Helicoverpa zea) and seasonal fluctuations in moth populations. The bats actually track local abundance of the moths within the regional landscape.

The larva of Helicoverpa zea is a major agricultural pest that is polyphagous (it can feed on a variety of different plants). It is considered to be one of the costliest pests in the United States, resulting in the loss of millions of dollar. 
Helicoverpa zea (Credit: cyanocorax)

An earlier study assessed the ecosystem services provided by this bat species within the Winter Garden region in Texas. They estimated that the bats provide on average services of 12% ($741,000) of the value of the annual cotton harvest. This accrues from reduced damage to cotton bolls and the prevention of 1-2 pesticide applications per year. 

An impressive value and this is only one agricultural branch researchers have looked at. The value of this bat with an appetite for things that eat crops is certainly much higher. As the authors of the study summarize:
Our results support growing evidence for the role of generalist predators, and bats specifically, as agents for biological control and speak to the value of conserving indigenous generalist predators.


Friday, October 12, 2012


A while ago I have posted on the prospects of environmental DNA probes when it comes to the detection of invasive species. Now researchers from the Central Michigan University presented yet another real-time, DNA-based testing method to detect invasive species. The research team successfully applied laser transmission spectroscopy (LTS) to detect species-specific DNA.

LTS is a quantitative and rapid technology for measuring the size, shape, and number of nanoparticles in a solution (see box for details). Because of this biding specificity, LTS is capable of distinguishing closely related species that differ by as few as 7 bp in a 32 bp species-specific gene region.

The group carried out a series of DNA detection (utilizing the DNA Barcode region) experiments using the invasive freshwater quagga mussel (Dreissena bugensis) to evaluate the capability of the LTS platform and its sensitivity. For the latter they extrapolated a concentration range for potential detection down to the picomolar range which makes the method very suitable for eDNA detection.

The researchers say this new easy-to-use, inexpensive technology paves the way for field-based identification of harmful species in samples from ships' ballast water, ports and other at-risk areas before contamination spreads into aquatic ecosystems.

Thursday, October 11, 2012

Promising sponges

Sponges are the most basal metazoans and consist of about 8,000 described species, with an estimated species number of more than 15,000. They are highly diverse, ecologically important and of significant commercial importance to the pharmaceutical and biomaterials industry. Thirty percent of all potential new natural medicine has been found in sponges. About 75% of the recently registered and patented active ingredients to fight cancer have been isolated from sponges. Furthermore, it appears that medicine derived from sponges can also be used for example for asthma or psoriasis treatment.

Harvesting of sponges is not an option for the production of biomedical substances. Neither are synthetic production or lab cultivation of bio-active components viable options. According to a couple of researches, isolating sponge cells and growing them in a bio-reactor under optimal conditions has the best chance of being successful. However, sponges are notoriously difficult to identify and any cell line needs to start with a properly identified donor organism. 

The Sponge Barcoding Project started a couple of years ago with the aim to cover all sponge taxa, and ranging in habitat from the marine intertidal to the deep-sea, as well as freshwater. The Sponge Barcoding Project was a major partner of the Marine Barcode of Life project (MarBOL). The goal was to obtain DNA Barcodes from 8,000 taxa to provide a basis from which more extensive sampling would be directed and routine identifications enabled. Recently described type specimens curated in associated museums were targeted first and will be supplemented with unequivocally identifiable taxa. 

Sponge Barcoding isn't as easy and as straightforward as one would hope. They host a large number of non-target macro- and microorganisms found in association with them. The DNA of these organisms can be co-extracted, and either co-amplified or preferentially amplified during PCR causing sequences to be difficult to read or belonging to non-target organisms. Moreover, for defense purposes, sponges produce potent bioactive compounds that can inhibit enzymatic reactions such as PCR. Another issue stems from the fact that some sponges show only very little or no variation in the standard COI region which led to developments of protocols that allow us to obtain longer sequences that contain sufficient variation. Often DNA barcodes are supplemented with ITS to enable unambiguous identifications. 

That might sound as if it is too difficult to justify further efforts but on the contrary: Despite all obstacles researchers have been able to obtain DNA Barcodes for a lot of sponges and the prospects for medical research are so high that the Sponge Barcode Project should rather be on top of the priority list when it comes to the assembly of DNA Barcodes of marine animals.

Tuesday, October 9, 2012

The deadliest sea snake

 ...is actually two species.

Enhydrina schistosa

Enhydrina schistosa, commonly known as the beaked sea snake, is a highly venomous species of sea snake common throughout the tropical Indo-Pacific.The venom of this species is made up of highly potent neurotoxins and myotoxins. The species is considered responsible for the vast majority of deaths from sea snake bites (up to 90% of all sea snake bites). It primarily inhabits coastal and inshore areas and can be abundant in estuaries and lagoons, where it poses a significant risk to fishermen handling nets. And now the surprise as this ‘species’ actually consists of two distinct lineages in Asia and Australia that are not even closest relatives. A group of researchers from Australia, Indonesia, and Sri Lanka were able to show convergence in the characteristic ‘beaked’ morphology of these species which is probably associated with the wide gape required to accommodate their spiny prey. Consequently they elevated the Australian “E. schistosa” to species status and provisionally referred to E. zweifeli. ("Zweifel" is the German word for doubt).

It would have been great if the authors had decided to include COI in their analysis as well (instead of cyt b for example). Their finds will have important implications for snake bite management as the only sea snake anti-venom available is raised against Malaysian E. schistosa. The inclusion of a DNA Barcode would have shown if it too can discriminate between the two species and would have made it a much better alternative to a multi-locus approach which is impracticable in every day use . In fact their mtDNA tree already shows that the Asian and Australian lineages have independent origins. This study will eventually lead to a description and a revision within the genus. DNA Barcodes of the types would be ideal and a great contribution to the DNA Barcode library. 

Given that snake venom has a strong phylogenetic component it is surprising that current treatment of snake bites seems to be unaffected by this. According to the authors the only thing "that has prevented this misidentification from having catastrophic medical implications, is that all sea snake venoms are very streamlined due to feeding on a single higher taxon (bony fish). Consequently all sea snake venoms tested to-date have been well-neutralised by the only available antivenom."

Friday, October 5, 2012

Happy Thanksgiving

Yes it's this time of the year - at least in Canada. Thanksgiving Day in Canada has been a holiday on the second Monday of October since 1957 unlike the US where it is always celebrated on the fourth Thursday of November.. For many here it is also the last long weekend before the long Winter arrives - time to get the cottage ready for the cold and - hopefully - snowy days. 

And yes - it is not a good season for Turkeys around here.

Invasive Seaweed

Invasive seaweed has the potential to harm a coastal ecosystem by growing over native seaweed, starving it of light and nutrients and thereby damaging a habitat and food source for many marine animals.

Last June for example beaches in Massachusetts have been blanketed with thickly packed red fibers resembling matted hair, causing a stink for beachfront residents and tourists alike. The Pacific native Heterosiphonia japonica was likely introduced through ship ballast water. It was first discovered at US coasts back in 2009 but had already caused a lot of damage on European Coasts in the early 1980's.

The new exotic red algae found in Europe
(a Gracilariopsis chorda; b Chondracanthus sp.; c Solieria sp.;
d Gelidium vagum)
European researchers have now discovered four new invaders in the Netherlands and France, three of them likely introduced after 2008.  None of them has become a nuisance yet but according to the authors these species could have the potential to modify shore ecosystems if they became truly invasive. The authors used the rbcL gene to identify red algal specimens that could not be morphologically identified as native species or known introductions.

Responsible for these new introductions into Europe are likely imports of Pacific oysters (Crassostrea gigas) , either directly from the north-western Pacific, or as a secondary introduction from a different region (in Europe or overseas). Indeed, all the sites where the new species have been observed were in the close vicinity (within a few hundred meters) of shellfish farming or trading facilities.

Wednesday, October 3, 2012

In the footsteps of Alfred Russel Wallace

Jumping spider
Peter Koomen / Naturalis)
A joint large scale expedition on the island of Borneo with researchers of the Malaysian nature conservation organization Sabah Parks and the Naturalis Biodiversity Center in The Netherlands just collected some 3500 DNA samples of more than 1400 species. Among these are likely 160 species new to science. They also came back with stunning photos of the species encountered.

The largest numbers of new species were found among spiders and fungi. Other new species include true bugs, beetles, snails, stalk-eyed flies, damselflies, ferns, termites and possibly a frog. Also a new location of the spectacular pitcher plant Nepenthes lowii has been found. 

The question is how many cryptic species among the ones collected are awaiting discovery? I am very much looking forward to the genetic analysis which hopefully will comprise DNA Barcodes aka COI as well. 

Megophrys nasuta (credit Joris van Alphen / Naturalis)
The plan is to use the genetic information to unravel relationships among the collected plants, fungi and animals. Relationships among the unique species on top of Borneo’s Mount Kinabalu will be compared to more widespread species on Borneo. This will answer the question whether these unique species have evolved long ago, or only recently. This will represent a follow up on Alfred R. Wallace who was the first to formulate a theory of evolution on Borneo.

Red mushroms
(Credit Luis Morgado / Naturalis)

For the fungi experts, the area was an Eldorado. The Hungarian mycologist József Geml says: “While the plant and animal life of this mountain has been the focus of numerous research projects, Kinabalu has remained terra incognita for scientific studies on fungi. It is difficult not to feel overwhelmed by this task. One of the manifestations of this diversity comes in the endless variety of shapes and colors that sometimes are truly breathtaking. While the detailed scientific work will take years, we already know that many of these species are new to science.

Barcode Bulletin Sep 2012

Hot off the press! The newest edition of the iBOL Barcoding Bulletin is out and yours truly was involved in its production as well. Have a look (just click on the image).

Tuesday, October 2, 2012

Ciona savignyi

Ciona intestinalis
Ciona savignyi is a sea-squirt native to the Asian Pacific. These ascidians are sessile filter feeders that unfortunately decided to feed on very small particles of sewage and waste, which led to the establishment of populations in regions all over the world.

Nobody can predict if invasive organisms will become nuisance species or not. We do, however, know some things already about Ciona savignyi, and its close cousin from Europe, Ciona intestinalis, both of which have a history as invasive species. Both species grow abundantly in certain man-made environments, floating docks, boat hulls, and on hanging aquaculture rafts. Interestingly their distribution is often consistent with hull fouling on ships and recreational boats as they seem to be the major vectors of introduction and spread. On natural surfaces they are less common, but C. intestinalis is known to cover eelgrass blades in some Scandinavian Fjords.

Early detection of these species would be very helpful but morphology-based ascidian taxonomy is a highly specialized discipline and the mis-identification of species has been, and remains, a significant problem due to a lack of reliable diagnostic morphological characters.

Researchers of the Cawthron Institute, Nelson and from the University of Waikato, Hamilton used DNA Barcodes to detect Ciona savigny in the waters around New Zealand. They also developed a simple PCR-based assay for discriminating between the two morphological very similar species Ciona intestinalis and Ciona savignyi. 

This is a great example how DNA Barcoding done the right way can aid in accurate species identification with applications in both biosecurity  programs and general research.

Monday, October 1, 2012

Blood flukes on an island

Schistosoma haematobium
Schistosomiasis is a parasitic disease caused by trematodes of the genus Schistosoma. There are four main species that infect humans. One of them is Schistosoma haematobium that causes urinary schistosomiasis.

Urinary schistosomiasis is often chronic and can cause pain, secondary infections, kidney damage, and even cancer. It has been infecting humans for at least 4000 years and had its own specific hieroglyph in ancient Egyptian. In the time before treatments were widely available, it was still so prevalent in Egypt that boys were traditionally expected to go through a “male menarche”—sometime during adolescence, it was normal for them to urinate blood. The infections continue to be a significant public health problem in much of Africa and the Middle East, second only to malaria among parasitic diseases. 

Bulinus sp.
The life cycle of the parasite involves an intermediate snail host (species of the genus Bulinus). Four weeks after the initial penetration into the snail the larval form - the cercariae - begin to be released. The free swimming  cercariae burrow into human skin when it comes into contact with contaminated water. They enter the blood stream of the host where they travel to the liver to mature into adult flukes. In order to avoid detection by the immune system inside the host, the adults have the ability to coat themselves with host antigens. After a period of about three weeks the young flukes migrate to the bladder to copulate. The female fluke lays as many as 3,000 eggs per day which migrate to the urinary bladder and ureters to be eventually released back into the water.

A parasitological survey was conducted on the Tanzanian island Mafia. Prior to the study a survey found that 7.5% of the School children had experienced symptoms of urinary schistosomiasis. However, parasitologically proven cases were lacking and earlier malacological surveys found only a few potential host species. Combined parasitological and malacological surveys were supplemented with observations on the compatibility of local Bulinus species with Schistosoma haematobium. The researchers used DNA Barcoding to identify both snail and schistosome. They found no evidence to suggest that Schistosoma haematobium is being actively transmitted on Mafia Island. With the substantial travel to and from the island, the refractory nature of local snails and evidence from DNA barcoding of schistosomes and snails, the authors conclude that the cases of urogential schistosomiasis are the result of imported infection.

I guess this is good news as the low prevalence allows for better control and chances are high that this parasite will not be established on the island.