Friday, December 18, 2015

School Malaise Trap Program - Fall 2015

We were scrambling a little in the last weeks but here they are (and all the participating schools have them already) - the results of our School program fall run:

In 64 traps students collected 750 specimens on average for the two week period in September. Our collections group sorted 47,711 specimens and selected 16,798  to be barcoded. Our final dataset was made up of 15,043 DNA Barcodes (not all  worked and short barcodes were discarded). Using BOLDs BIN analysis we could  determine that the record number of 3,515 species were collected over the two week period of the program, 247 of which were brand new to BOLD. The map below shows all of these collection sites, which include elementary schools, secondary schools, and comparison sites (blue markers). You might notice that we also had some participants from the US. A shout out to our friends from some of the San Diego Libraries.

Our overall pie chart shows the typical species composition (largely grouped in orders) although this time the dipterans are not as predominant as they were in other years and runs. We caught almost as many different hymenopteran species. Mind you this is not a figure that corrects for abundance as flies clearly dominate each catch by their numbers.

Once more a great accomplishment by a large number of young citizen scientists. After three years still many surprises and new finds. Impressive.

Winter Bulletin is out

It's time for our Winter Issue of the Barcode Bulletin. For me that also means that I am about to head out for two weeks break. Consequently, posting will be rather light before we pick up speed again in early January.

Christmas greetings will follow in another post closer to crunch time. Meanwhile enjoy reading our jam-packed issue:

Thursday, December 17, 2015

Citizen science to protect trees

Ablaze with colour in autumn and carpeted with bluebells in spring, native woodlands are one of Britain's most prized natural treasures. New research is showing that the public together with scientists can play a vital role in their protection. 

A study, carried out by scientists at Forest Research and Rothamsted Research in the UK, involved a survey of the Acute Oak Decline (AOD) disease which has affected oak trees across England and Wales. AOD reduces oak trees' ability to take up food and water, and has the potential to kill trees in 4-6 years. This threatens indigenous woodland and the many species of plants and animals that rely on oak trees for food and protection.

To make the survey even more far-reaching, the researchers also gathered sightings of AOD reported by concerned public volunteers. These 'citizen scientists' followed online instructions, and some even had training from Forest Research professionals on how to identify disease symptoms and to take non-destructive swab samples for experts to verify. The confirmed public sightings were compared with those of the scientific survey to determine how reliable they were.

This research provided a unique opportunity not only to map the known extent of AOD in the UK but to compare the results from historical and current records held by FR which were submitted by citizen scientists to that of data from a systematic and scientifically robust survey.

The results showed clear similarities between reports gathered from the scientific survey and those verified from the public volunteers. Both volunteers and scientists found AOD in central and southern England, whereas it was rare in Wales and in more northern and southwest areas of England. Help from the public can therefore play an important role in informing policy and management of woodland conservation, such as in helping scientists to predict which areas are at risk of AOD and other tree diseases, and preventing their spread.Consequently the researchers want to continue to involve citizen scientists in their work:

Observatree, an EU-funded citizen science project led by Forest Research which is training volunteers to identify and report tree pests and diseases. This approach can provide an efficient early warning system for pests and diseases, and our findings suggest volunteer detections can also be used to define the distribution of affected woodland.

Wednesday, December 16, 2015

If Nemo's kids can't find home

The transition from a pelagic to a benthic lifestyle is a crucial phase in the life cycle of many marine organisms. During early stages of development, dispersal of planktonic larvae may be mostly driven by currents; however, larvae progressively develop behavioural and physiological competencies that allow them to locate, orient towards and selectively settle in suitable benthic habitat. Competencies acquired during development include increased body size, development of functional fins and strong musculature, as well as sensory capabilities necessary for navigation and habitat selection. This set of adaptations means that settlement is far from a stochastic event.

Research has shown that acoustic cues help in the settlement of marine fishes and some invertebrates. Electrophysiological studies also revealed that the sense of hearing becomes more important throughout larval development and that at this particular life stage they are able to hear particular frequencies, an ability lost later in life. It is also known that some fish species have a very narrow window of competency for settlement. It seems likely that both findings are connected and that hearing guides little fish toward their future home.

A new study published today provides some more proof for the assumption that the interpretation of normal ocean sound cues helps juvenile fish to find an appropriate home. However, tests conducted as part of the study also showed that fish were completely confused under the levels of CO2 predicted to be found in oceans by the end of the century as a result from Ocean acidification:

Here we show that larvae of a catadromous fish species (barramundi, Lates calcarifer) were attracted towards sounds from settlement habitat during a surprisingly short ontogenetic window of approximately 3 days. Yet, this auditory preference was reversed in larvae reared under end-of-century levels of elevated CO2, such that larvae are repelled from cues of settlement habitat. These future conditions also reduced the swimming speeds and heightened the anxiety levels of barramundi. Unexpectedly, an acceleration of development and onset of metamorphosis caused by elevated CO2 were not accompanied by the earlier onset of attraction towards habitat sounds. This mismatch between ontogenetic development and the timing of orientation behaviour may reduce the ability of larvae to locate habitat or lead to settlement in unsuitable habitats. 

There is a nice little video that explains all this in simpler terms:

Tuesday, December 15, 2015

Combining Public Health Education and Research

Chagas disease is caused by a parasitic protozoan (Trypanosoma cruzi) and transmitted via the so called kissing bugs (Triatominae) Due to the success of community based surveillance and collection in Central and South America, researchers from Texas A & M University set up a citizen science program to gain insight into the distribution and infection prevalence of the vector insects in Texas.

The researchers used printed pamphlets, phone communication, an educational website with a dedicated email address and local news station announcements to provide public information about the program. Citizens were encouraged to submit triatomine insect specimens. Submitters were informed of the risk of Chagas disease and cautioned not to touch the insects with bare hands. Each submission was required to include the date, time and location of capture and whether the insect was alive or dead.

Each insect was identified to species, measured, sexed and dissected. DNA from the insect gut was extracted and tested for the presence of the parasite. Any insects reported to have fed on humans were sent to the state health department for further processing. Submitters were notified of the species and infection status of their sample. An interactive map of the location of all submissions is published on the project's website.

Over 4000 emails were received from the public over the course of the 2 years, and 1980 kissing bug samples comprising seven species submitted. Of the submitted insects, 25% were found in dog kennels, 19% in patios or porches and 11% inside homes. In total, 375 citizens submitted samples, the majority submitting only one insect. Citizens submitting >20 samples were most likely to have found them in their dogs sleeping quarters. Tests for Trypanosoma cruzi were carried out on 694 of the insects and 63% were found to be infected. The geographic distribution of the insects was similar to previous documentation spanning 8 decades, suggesting that citizen collections are a valid way to document insect distribution in future.

Using public citizens for this kind of initiative means that insects will only be found in places citizens have visited. This does, however, create a unique sample of the insects likely to be encountered by the public, which is a useful sub-set for studies of disease vectors. Using DNA-based identification of samples also negates observer error which can be a risk of citizen identification. Finally the set up and running of the program strengthens relationships between researchers, health departments, disease control centers, clinical vets and the public, and provides a resource of public information on a local illness.

Monday, December 14, 2015

Ballast water

Maritime transport is considered one of the most important ways that native species are moved between marine regions. The trip can be especially successful if these species latch on to the vessel's anchors or chains, or even if they travel in the ship's ballast water tanks. Each year, between 2.2 and 12 billion tons of water are transported around the oceans of the world in these ballast water tanks which also serve as a means of transport for about 7,000 species per day. In a survey colleagues found more than 1,000 taxa of living specimens in ballast tanks of vessels arriving in European ports.

A golden rule for successful invaders is ‘the more tolerant are the more dangerous'. Therefore, migrants that survive long cross-latitudinal voyages within ballast tanks should be of particular concern as potential invaders. Identifying such species is crucial for conducting reliable risk analyses, preventing expansions and developing efficient control methods. However, many species transported in ballast water as eggs or larvae are often very difficult to identify.

In order to identify which organisms are most capable of tolerating non-native waters and are thus the most invasive, a team of researchers from Spain and Lithuania applied metabarcoding of the environmental DNA present in 70 m3 of ballast water of the scientific research vessel Polarstern. The tanks were filled in the North Sea and the vessel traveled from Bremerhaven (Germany) and Cape Town (South Africa). Over the long travel distance the ballast water was subjected to extreme temperature variations in addition to anoxic conditions. 

Organisms that were alive upon entry into the tank in Bremenhaven could have been subjected to conditions of stress likely resulting in their death, thus meaning that the number of DNA molecules within the tank would decrease over the course of a trip. However, this is not what happened to a mudsnail (Peringia ulvae). The researchers found that the number sequences of a particular haplotype increased during the journey.

Although this is not conclusive evidence confirming that the little mollusk is alive but it certainly confirms the resistance of its DNA to adverse conditions. Up until now there has not been any evidence of the presence of this small snail outside of its natural habitat, although some studies have indeed described its ability to tolerate diverse ecological conditions.

The results of this study indicate the high likelihood of species survival in ballast water or ballast sediments on cross-regional voyages. It can therefore be used for the species-specific risk assessments required by the Ballast Water Management Convention and for prioritizing species of greatest management concern.

Friday, December 11, 2015

Citizen Science in Malaysia

Over the past 50 years, Southeast Asia has suffered the greatest losses of biodiversity of any tropical region in the world. Malaysia is a biodiversity hotspot in the heart of Southeast Asia with roughly the same number of mammal species, three times the number of butterfly species, but only 4% of the land area of Australia. Consequently, in Malaysia, there is an urgent need for biodiversity monitoring and also public engagement with wildlife to raise awareness of biodiversity loss. Citizen science is “on the rise” globally and can make valuable contributions to long-term biodiversity monitoring, but perhaps more importantly, involving the general public in science projects can raise public awareness and promote engagement. Butterflies are often the focus of citizen science projects due to their charisma and familiarity and are particularly valuable “ambassadors” of biodiversity conservation for public outreach.

The Peninsular Malaysia Butterfly Count is a great example for citizen science involving school children. We were following their work through Facebook already for a while and it is wonderful that all this work and its results now made it into the scientific literature through an article just published in Pensofts Biodiversity Data Journal.

Congrats to John Wilson and his team - keep up the good work. Here's their summary:

1) The level of participation in the first Peninsular Malaysia Butterfly Count was encouraging, but reaching and engaging rural communities remains a challenge.

2) The non-lethal DNA barcoding approach for species identification worked effectively, however, protocols could be improved to limit the number of returned samples which could not be identified. The family-level identification guide could use some improvement but provides an important educational tool for the participants.

3) The sampled butterflies revealed that widely distributed, cosmopolitan species, often recently arrived to the peninsula or with documented "invasive" potential, dominate the habitats sampled by the participants. Data from the first Butterfly Count helps establish a baseline from which we can monitor changes in butterfly communities in Peninsular Malaysia.

Thursday, December 10, 2015

Complementary and alternative medicines

Globally, there has been an increase in the use of herbal remedies including traditional Chinese medicine (TCM). There is a perception that products are natural, safe and effectively regulated, however, regulatory agencies are hampered by a lack of a toolkit to audit ingredient lists, adulterants and constituent active compounds.

A new study just published in Nature Scientific Reports does just that (including metabarcoding) and the results are - perhaps not surprising - pretty alarming. Researchers of Curtin University, Murdoch University and the University of Adelaide found that 90 % of 26 widely available medicines (in Australia) tested were not fit for human consumption. Half contained illegal substances, including toxic metals, prescription medications, stimulants and animal DNA, none of which were listed on the product's label.

Arsenic, cadmium and lead were found in some of the Chinese medicine. One of the herbal concoctions contained over 10 times the recommended daily limit for arsenic exposure. Another contained strychnine, which is used as a rat poison and at lower levels as a performance-enhancing drug. The researchers also found one of the herbal medicines for sale had trace amounts of snow leopard DNA in it. In addition they found DNA from pit vipers, frogs and trace amounts of cat and dog DNA. Whether the animal products were primary ingredients or the result of a poor manufacturing processes is yet to be determined.

The researchers were especially concerned about contamination with undisclosed pharmaceuticals. Over-the-counter drugs like paracetamol and ibuprofen were found but also steroids, blood thinner warfarin and even sildenafil, the active ingredient in Viagra.

Here the summary of the paper:
This study presents genetic, toxicological, and heavy metal data that should be of serious concern to regulatory agencies, medical professionals and the public who choose to adopt TCM as a treatment option. Of the 26 TCMs investigated, all but two can be classified as non-compliant on the grounds of DNA, toxicology and heavy metals, or a combination thereof. In total, 92% were deemed non-compliant with some medicines posing a serious health risk. The multi-tiered approach outlined in this study provides a much-needed auditing toolkit that should swiftly form the basis of best-practice pharmacovigilance across the CAM  [complementary and alternative medicines] sector.

Wednesday, December 9, 2015

Lots of marine species actually unprotected

The increase in the number MPAs in recent years is encouraging, but most of this increase has come from a few very large MPAs. Those very large MPAs provide important value, but they can be misleading in thinking that biodiversity is being well protected because of them. Species all around the planet need protection, not just those in some locations. 

The first comprehensive assessment of protected areas coverage on marine life says that more than 17,000 marine species worldwide remain largely unprotected

The authors of the study looked at the ranges of some 17,348 species of marine life, including whales, sharks rays and fish, and found that 97.4 percent have less than 10 percent of their range represented in marine protected areas. Nations with the largest number of "gap species" or species whose range lie entirely outside of protected areas include the U.S., Canada, and Brazil. 

Despite these dismal and somewhat shameful results, the authors say the study underscores opportunities to achieve goals set by the Convention on Biological Diversity to protect 10 percent of marine biodiversity by 2020. For example, the majority of species that were considered very poorly represented (less than two percent of their range found in marine protected areas) are found in exclusive economic zones. This suggests an important role for particular nations (see above) to better protect biodiversity.

As most marine biodiversity remains extremely poorly represented, the task of implementing an effective network of MPAs is urgent. Achieving this goal is imperative for not just for nature but for humanity, as millions of people depend on marine biodiversity for important and valuable services.

Monday, December 7, 2015

Combat fish food fraud

Over the years I have presented several studies that showed ongoing food fraud in the seafood trade and how DNA Barcoding helped to unravel these cases. Now a large multi-species survey of fish labeling accuracy indicates a marked reduction of seafood mislabeling in supermarkets, markets and fishmongers in the EU.

Scientists in six European countries tracked samples of the mostly commonly consumed fish, including cod, tuna, hake and plaice, after a series of studies going back 5 years had shown mislabeling in up to 40% of cases.

Of the 1 563 DNA sequence samples examined, just 77 (4.9%) proved to be mislabeled. Most commonly mislabeled was anchovy (15.5%), hake (11.1%) and tuna (6.8%). By contrast only 3.5% of cod and 3% of haddock was  wrongly labeled. 

The study argues that this positive trend is due to a combination of transnational legislation, governance and public outreach, which has forced new regulation and self-regulation, and it contrasts the European 'turn-around' with the experience of the United States, where improvements appear more sluggish.

Genetic identification methods have progressively exposed the inadequacies of the seafood supply chain, raising awareness among the public, and serving as a warning to industry that malpractice will be detected. This evidence indicates we are now on the road to greater transparency, which should help the management of exploited stocks worldwide, but further standardised studies on a greater range of food provision channels, such as restaurants and auctions, are warranted, in order to have a complete understanding of the current state of the trade.

Friday, December 4, 2015

Topical Issue on DNA Barcoding of Fishes

A new special issue dedicated to FishBOL work has been published in the journal DNA Barcodes. Quite a few articles on recent research of the global fish barcoding community. Have a look:

Thursday, December 3, 2015

Quantitative metabarcoding

It is a bit of a holy grail for metabarcoding and a dream of many: Using it not only to determine species identities but also for quantifying relative species abundances. It is widely accepted that metabarcoding has its limits and is biased both biologically and technically. For example, chimeric sequences, contaminants and clustering algorithms can bias even the most basic outputs of DNA metabarcoding studies such as species richness. This becomes very problematic if one tries to infer abundance from the proportions of species DNA. Attempts have been made to extrapolate differences in mass or abundance of species through differences in sequence read abundance but biases have been repeatedly reported.

Previous attempts to control biasing factors in DNA metabarcoding studies have primarily focused on correcting for a single source of bias, or altering protocol steps that are known to introduce bias...An alternative approach to correcting for individual biases is to create control materials for target organisms, which when sequenced alongside environmental samples can be used to create correction factors that account for multiple sources of bias simultaneously.

A new study that just showed up in the accepted article section of Molecular Ecology Resources went the latter route and used sequencing of 50/50 mixtures (target species/control species) to establish relative correction factors (RCF) that account for multiple sources of bias and are applicable to field studies.

The colleagues focused on a rather small model system containing a few fish and a small prey library for Pacific harbour seals. However, they also applied the prey library derived correction factors to some wild seal scat samples to determine the impact of the correction method on a real world scenario. Their results show that the 50/50 RCF approach represents an effective tool for evaluating and correcting biases for the model chosen and likely for other studies as well. The authors also clearly state that their new method will not solve the problem for all possible scenarios and that there will be lots of cases where it is simply unrealistic to expect accurate estimates of species proportion based on DNA sequence read abundances.

However, in study systems focused on a limited number of species which have conserved barcode priming regions, 50/50 RCFs offer potential to improve proportional estimates by accounting for multiple sources of bias. The 50/50 RCF approach will be particularly useful when biases to sequence read abundance are substantial and the resulting species correction factor magnitudes are large. Even when it is not possible to generate a complete tissue library, a 50/50 RCF library consisting of a subset of key species could be used to screen for large species-specific biases and aid in the interpretation of sequencing results.

Tuesday, December 1, 2015

We're crowdfunding!

Dear Colleagues,

Today is Giving Tuesday, the global day of giving, and we are excited to announce that this year the School Malaise Trap Program will be hosting a crowdfunding campaign through the University of Guelph
Over the past three years, the program has become an outstanding success through the constant dedication of educators, students, and supporters of the Biodiversity Institute of Ontario. Through our generous funders we have been able to reach nearly 15,000 students and over 250 schools across Canada! Furthermore, the scientific findings associated with the program are quite impressive. Over 6,500 arthropod species have been collected by participants, with 1041 of those species being new to BOLD.
As resources diminish, we are asking for support from generous donors like you so that we may keep the program alive! This year we are hoping to raise at least $10000 in order to keep the program free for participants (average cost = $1000 per participant). For more information about our program costs and our goals, please click here.
Every little bit helps! If each person who receives this email donates $15.43, we would be able to reach our goal TODAY! We ask that you kindly consider donating as well as spreading the word by forwarding this email or sharing it via social media. 
To donate, please click here.

All donations are eligible for a tax receipt, and you can feel good about continuing to bring modern biodiversity science to students and educators across Canada. We thank you in advance for your contribution to keep this valuable educational opportunity alive!
The School Malaise Trap Program Team
In the past three years, over250 schools and almost15,000 students have contributed 68,000 specimens, representing6,500 different species, to BOLD (BIO’s online barcode reference library). 1,041 of these species were NEW to BOLD, having never been DNA barcoded before!
Learn More about the School Malaise Trap Program

Thursday, November 26, 2015

Charlotte's Web unraveled

credit Scott Camazine
As dominant predators of arthropod communities in natural and agricultural ecosystems, spiders can be important ecological indicators that reflect habitat quality and change. Monitoring the species diversity and abundance of spider assemblages facilitates natural resource management. However, spiders are enormously diverse (~ 45,000 described species) and many can be difficult to identify.

A spider's web contains traces of its DNA, as well as the DNA of whatever prey got stuck in the web. Therefore, it represents a great source for noninvasive genetic sampling and enables biomonitoring without the need to directly observe or disturb target organisms. The question is if there is sufficient predator and prey DNA in the web to allow for reliable species identification. 

A group of US researchers put this to the test and published their finds in PLoS ONE. For the study, the colleagues studied the webs of a couple of black widow spiders that were kept in separate enclosures. They fed each spider with crickets and, several days later, removed the webs from the enclosures to extract DNA from the web samples. The used DNA Barcoding to test if they were able to obtain DNA of both species. It is remarkable that no fancy eDNA or metabarcoding protocol was used - simple PCR and Sanger sequencing.

There experiments were quite successful. In one case a sample was collected 88 days after the death and removal of both spider and prey, demonstrating surprising persistence of web DNA. Of course this was a laboratory based experiment which needs to be tested with field collections where DNA-degrading conditions such as heat, moisture, and light will certainly have an effect on the quality of the available DNA. Nevertheless, this proof of concept is really promising given how sensitive modern genetic tools are.

Wednesday, November 25, 2015

Community-wide Arctic DNA barcode library

Today, Molecular Ecology Resources just released a publication that establishes the to-date most comprehensive library of DNA Barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively-studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland.

In an earlier study the site was used to understand how feeding interactions are structured by focusing on one of the simplest food webs on Earth: the moths and butterflies of Zackenberg Valley, as attacked by their specialist enemies, parasitic wasps and flies developing on their host, killing it in the process. The work was the result of a five-year exploration of insect food webs of a rather simple system with perhaps only a handful of species to keep track of. A food web structure of manageable complexity which made researchers much more confident to have captured the full system and to have ruled out interactions that were not part of it. It turned out that this allegedly simplest food web one could possible find in the world was far more complex that previously thought. The game changer was the inclusion of DNA Barcoding technology and it indeed changed every measure of the food web structure with three times as many interactions between species as known before. On average, most types of predator proved less specialized than assumed, and most types of prey were attacked by many more predators than previously thought.

Now the colleagues took it up a notch. They barcoded 403 terrestrial animal and 160 vascular plant species recorded by morphology-based techniques. To demonstrate the utility of this reference library, the researchers used it to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers.

Drawing on this material, we estimate the coverage of previous morphology-based species inventories, derive a snapshot of faunal turnover in space and time, and describe the abundance and phenology of species in the rapidly changing arctic environment.

The Malaise trap catches revealed 122 BINs (aka species) that hadn't been not detected by past sampling  efforts. Interestingly, the arctic insect community was strongly dominated by a very few hyperabundant taxa. Only five BINs were represented by more than ten individuals per trap day during at least one season – but of these, the two most abundant ones accounted for 5230 and 2256 individuals.

The authors also found substantial species turnover in space and time:
Focusing on the one year (2014) in which both Trap A and B were operated, we detected a difference of more than half of local species over a distance of less than 1 km (Fig. 1; Appendix S5). Examination of patterns in time similarly revealed large turnover. Year 2013, which was characterized by an early spring and unusually little snow, was different from the years of 2012 and 2014 which shared a late snow melt.

The new wealth of data and the fact that future research can build on a comprehensive barcode reference library allows the colleagues to go back to their foodweb analysis even though it will likely mean that the complexity will strongly increase. Nevertheless, understanding who feeds on whom and how often is the basis for understanding how nature is built and works.

Tuesday, November 24, 2015

The Science Borealis Readers Survey

Today I have a small request for all my readers.

I've teamed up with Science Borealis, Dr. Paige Jarreau from Louisiana State University and 20 other Canadian science bloggers, to conduct a broad survey of Canadian science blog readers. Together we are trying to find out who reads science blogs in Canada, where they come from, whether Canadian-specific content is important to them and where they go for trustworthy, accurate science news and information. Your feedback will also help me learn more about my own blog readers. 

It only take 5 minutes to complete the survey. Begin here:

If you complete the survey you will be entered to win one of eleven prizes! A $50 Chapters Gift Card, a $20 surprise gift card, 3 Science Borealis T-shirts and 6 Surprise Gifts! PLUS everyone who completes the survey will receive a free hi-resolution science photograph from Paige's Photography!  

Thanks so much for taking part.

Monday, November 23, 2015

More than half of all Amazonian tree species may be globally threatened

Amazonian forests have lost ~12% of their original extent and are projected to lose another 9 to 28% by 2050. The consequences of ongoing forest loss in Amazonia (here all rainforests of the Amazon basin and Guiana Shield) are relatively well understood at the ecosystem level, where they include soil erosion, diminished ecosystem services, altered climatic patterns, and habitat degradation. By contrast, little is known about how historical forest loss has affected the population sizes of plant and animal species in the basin and how ongoing deforestation will affect these populations in the future.

In a new study, published this week in the journal Science Advances, a research team comprising 158 researchers from 21 countries compared data from forest surveys across the Amazon with maps of current and projected deforestation to estimate how many tree species have been lost, and where.

Their results show that 36-57% of the Amazon's estimated 15,000 tree species likely qualify as globally threatened under IUCN Red List of Threatened Species criteria. Because the same trends observed in Amazonia apply throughout the tropics, the researchers argue that most of the world's more than 40,000 tropical tree species likely qualify as globally threatened.

Fortunately, the authors also report that protected areas and indigenous territories now cover over half of the Amazon Basin, and contain sizable populations of most threatened tree species.

This is good news from the Amazon that you don't hear enough of. In recent decades Amazon countries have made major strides in expanding parks and strengthening indigenous land rights. And our study shows this has big benefits for biodiversity.

However, parks and reserves will only prevent extinction of threatened species if they suffer no further degradation. The authors caution that Amazonian forests and reserves still face a barrage of threats, from dam construction and mining to wildfires and droughts intensified by global warming, and direct invasions of indigenous lands.

It's a battle we're going to see play out in our lifetimes. Either we stand up and protect these critical parks and indigenous reserves, or deforestation will erode them until we see large-scale extinctions.

Friday, November 20, 2015

Incentives to adopt DNA barcoding

credit: New York Times
When it comes to DNA Barcoding in the media the really big stories mainly relate the seafood market. That started with the famous 'Sushigate' , now 6 years ago, where two high school students used the method to show that many items on menus in seafood restaurants were simply mislabeled. 

The increasing spate of species substitution and mislabelling in fish markets has become a concern to the public and a challenge to both the food industry and regulators. Species substitution and mislabelling within fish supply chains occurs because of price incentives to misrepresent products for economic gain. 

It seems only a matter of time that DNA Barcoding will be adapted as regular means of species identification in the seafood business and in fact regulatory agencies such as the US FDA have adopted it already. However, what would be the incentives to adopt the technology for supply chain monitoring is the technology actually feasible for a retailer?

A new study published in Genome tries to answer these questions:

However, the adoption of these authenticity technologies depends also on economic factors. The present study uses economic welfare analysis to examine the effects of species substitution and mislabelling in fish markets, and examines the feasibility of the technology for a typical retail store in Canada.

The study shows that DNA Barcoding is feasible for a typical retail store only if done in a third party laboratory. Considering fixed and other associated costs it is not doable on an individual retail store level.

Given the magnitude of the fixed costs and low food safety risk associated with fish species substitution in Canada presently, the adoption of DNA barcoding technology, particularly by small-scale retailers, is only likely if external testing facilities are available. In the longer run, the potential for retailers to pool resources by investing jointly in industry testing facilities may be worthy of examination, for example, small independent retailers may find it worthwhile to cooperate in the establishment of shared testing infrastructure. Although not directly derived from the analysis, large-scale retail stores with multiple outlets could spread the fixed costs associated with testing infrastructure over multiple stores with testing occurring at the retailers’ central warehouse. Indeed, this would be the most likely scenario for large retailers operating centralized distribution systems.

Good news for all the food testing labs that have been bubbling up recently especially if governments react to raising consumer concern and start changing the regulatory landscape with respect to food fraud. 

Thursday, November 19, 2015

Perhaps some interesting reads

Today is a day for some shameless self-advertisement. Aside from writing a blog, running educational programs and spreading the word about biodiversity science I actually sometimes find the time to do some research and eventually that science might turn into papers (Yeah!).

In the past weeks three new publications saw the light of day. Here they are for your entertainment provided you like this DNA Barcoding stuff:

(1) Adamowicz SJ, Steinke D (2015)

Genome - online early
Here, we advance our opinion that increased global participation in genetics research is beneficial, both to scientists and for science, and explore the premise that DNA barcoding can help to democratize participation in genetics research. We examine publication patterns (2003-2014) in the DNA barcoding literature and compare trends with those in the broader, related domain of genomics. While genomics is the older and much larger field, the number of nations contributing to the published literature is similar between disciplines. Meanwhile, DNA barcoding exhibits a higher pace of growth in the number of publications as well as greater evenness among nations in their proportional contribution to total authorships. This exploration revealed DNA barcoding to be a highly international discipline, with growing participation by researchers in especially biodiverse nations. We briefly consider several of the challenges that may hinder further participation in genetics research, including access to training and molecular facilities as well as policy relating to the movement of genetic resources.

Oceanography 28(3):158–189
At the beginning of the Russian–American Long-Term Census of the Arctic (RUSALCA) program in 2003, the composition and characteristics of the Pacific Arctic marine fish fauna and distribution of the species were poorly known compared with knowledge on the fish fauna of warmer waters. The mission for ichthyological investigations in the RUSALCA program has been to provide information necessary to construct zoogeographic and taxonomic baselines against which change may be detected. Our methods have involved examining historical fish collections in museums and identifying fresh samples secured on RUSALCA scientific expeditions and those of other programs, and DNA barcoding. This paper presents the first modern, comprehensive, well-founded inventory of the marine fish species in the Pacific Arctic region and its subregions; evaluates each species’ zoogeographic pattern, primary distribution, biotype, and life zone; and highlights some of the positive results of our investigations in the first decade of the program as well as new and persistent problems identified that need further investigation.

(3) Raupach MJ, Barco A, Steinke D, Beermann J, Laakmann S, Mohrbeck I, Neumann H, Kihara, TC, Pointner K, Radulovici A, Segelken-Voigt A, Wesse C, Knebelsberger T (2015)
PLoS ONE 10(9): e0139421
Here we present a comprehensive DNA barcode library of various crustacean taxa found in the North Sea, one of the most extensively studied marine regions of the world. Our data set includes 1,332 barcodes covering 205 species, including taxa of the Amphipoda, Copepoda, Decapoda, Isopoda, Thecostraca, and others. This dataset represents the most extensive DNA barcode library of the Crustacea in terms of species number to date. By using the Barcode of Life Data Systems (BOLD), unique BINs were identified for 198 (96.6%) of the analyzed species. 

Wednesday, November 18, 2015

Meetings, meetings, meetings

November is DNA Barcode meeting month it seems.

Just last week NorBOL held a symposium  on Biodiversity and DNA Barcoding in Trondheim. Nearly 100 participants from Norway, Sweden, Canada, Finland, Germany, Czech Republic and the UK came to Norway for this event. More details can be found in a report that was just published at the NorBOL website

Another meeting will happen early next week (23-25 Nov). MexBOL will have its 3rd annual meeting at UNAM in Mexico City. Here is a preview of the program:

Tuesday, November 17, 2015

Two hungry caterpillars

Helicoverpa armigera
The Old World bollworm, Helicoverpa armigera, and the corn earworm, Helicoverpa zea  are considered two of the most important agricultural pests in the world. Both of them are highly polyphagous and the greatest damage is inflicted on cotton, tomatoes, maize, chick peas, alfalfa and tobacco. However, in total Helicoverpa armigera feeds on hosts in 68 plant families and Helicoverpa zea on hosts in 36 plant families. Now these are some really hungry caterpillars.

Identifying these two species is difficult. Adults can only be separated by complex dissection, and larvae cannot be identified to species using morphology. In the past geographic origin was used for identification in most instances but recently several studies showed that both species occur in the same regions. A PCR-RFLP assay using COI, and cytochrome b (Cyt b) was developed to distinguish between the two species and a few other congeners but it turns out that some species such as Chloridea virescens generate RFLP patterns identical to those for Helicoverpa armigera.

A new study published in PLoS ONE now introduces a real-time PCR assay to diagnose and separate the two species. The assay is based on ITS-2 and 18S rRNA but all control specimens were initially identified using some morphology and DNA Barcoding. 

The assay can be completed in 50 minutes when using isolated DNA and is successfully tested on larvae intercepted at ports of entry and adults captured during domestic surveys. We demonstrate that the assay can be run in triplex with no negative effects on sensitivity, can be run using alternative real-time PCR reagents and instruments, and does not cross react with other New World Heliothinae.

This is certainly a significant time saving over e.g. DNA Barcoding, where sequencing of the final PCR product is required. As this is also the most expensive step in the process there is also some significant cost saving involved. Furthermore, the assay is capable of providing a correct diagnosis even in the presence of other species. However, the new method has a few limitations:

Although the assay was tested with a variety of other Helothinae, including other Helicoverpa, caution should be used when applying these protocols outside of the New World. 
Mixed template testing demonstrates that the real-time assay developed here is not applicable for diagnosing bulk samples.

Nothing is perfect but these are rather cautionary remarks than real limitations. After all the test was developed for a very specific task and that's what it does with remarkable precision.

Monday, November 16, 2015

Invasive freshwater species in Europe’s lakes and rivers

Freshwater ecosystems suffer from greater loss of biodiversity than most terrestrial ecosystems, mainly due to human activities including the introduction of species outside their natural range. Twenty percent of species extinctions are caused by invasive alien species.

A new study analysed the spatial and temporal patterns and trends of the main pathways and gateways of alien species in Europe, using the European Alien Species Information Network (EASIN) inventory. This inventory currently includes over 750 freshwater species reported as aliens (established or suspected) in European inland waters. The study is the first pan-European assessment of both the main pathways and gateways of first introductions for freshwater alien species in Europe. Its results could greatly help achieve the Aichi Biodiversity Target 9 regarding the prevention and control of invasive alien species.

The study found a marked increase in the introduction of freshwater alien species in Europe over the past 60 years, largely as a result of globalisation. The results identified escape from aquaculture facilities, releases in the wild due to pet/aquarium trade and stocking activities as the main pathways of alien species introduction in European lakes and rivers. Germany, the UK and Italy are the main entry gateways. Most of the initial introductions in Europe come from aquaculture, which is one of the fastest-growing sectors of the world food economy. Aquaculture is trailed by aquarium trade, a multi-billion dollar industry which has also seen remarkable growth in recent years. 

The authors recommend tightened controls, and improved prevention and management measures in order to halt the increasing trend of freshwater alien species introductions in Europe. They also note that public education could greatly help increase awareness of the risks for freshwater ecosystems.

Since a clear policy for the prevention, containment and monitoring of invasive alien species is finally available in Europe, adequate measures tackling priority pathways and gateways of introductions in Europe are expected to be implemented in the near future. 

Well, I can only hope these include DNA-based identification methods such as DNA Barcoding.

Friday, November 13, 2015

DNA Barcoding, Game-Changing Research

Research Matters is a public outreach initiative by the Council of Ontario Universities. It explores how Ontario university research affects everyday life, and improves the ways people live, work and play. In spring the Research Matters team launched a fun online campaign to highlight the 50 game-changing discoveries made in the province’s universities over the last 100 years. The public was asked to vote for their favorites and yesterday the top five were announced. The top five innovations selected, in no particular order, are:

Fighting Gravity: Wilbur Franks, University of Toronto, invents the first anti-gravity or G-suit used in combat, and it is still the foundational design for contemporary fighter-pilot and astronaut pressure suits.

Treating Diabetes: Frederick Banting, Charles Best, J.J.R. Macleod and J.B. Collip, University of Toronto, Western University, develop insulin to treat diabetes, a life-saving discovery for millions.

Reinventing the Potato: Gary Johnston, University of Guelph, develops the yellow-fleshed Yukon Gold potato – its popularity making it a household name.

Breathing Easier: Fred Possmayer, Western University, develops a technique to purify and sterilize lung surfactant – a substance that allows lungs to expand and breathe. It has saved the lives of countless premature babies and is used by 99 per cent of the neonatal intensive care units in Canada.


Digitizing DNA: Paul Hebert, University of Guelph, proposes DNA barcoding for species identification, with applications from protecting global biodiversity to curbing food fraud.

Now that is nice. The University of Guelph lands twice among the winners, and remarkably the rather young innovation DNA Barcoding shows up at the top. Not that this competition has any global relevance but we are proud that our research is highly regarded by the public in our province. 

Thursday, November 12, 2015

High school DNA Barcoding project in Siemens Competition

The Siemens Competition in Math, Science and Technology is one of the premier competition the United States. It promotes excellence in math, science and technology. High school students submit innovative individual and team research projects to regional and national levels to compete for college scholarships ranging from $1,000 up to $100,000.

Among the semi-finalists were three students from a high school in Tenafly New Jersey. They were recognized for their research project, "Assessment of Sulfur Dioxide Air Pollution in Central Park through DNA barcoding of Key Indicator Lichen Specimens."

For the project, they chose to determine sulfur dioxide air pollution levels in various areas of Central Park in New York City by examining the concentration of lichen species. Lichens have a specific range of sulfur dioxide that they can tolerate, If there is a concentration of lichens with a high tolerance for sulfur dioxide in a specific area, it can be concluded that there is a high level of pollution in that zone.

The team, which began research in September 2014, traveled to Central Park to collect samples from rocks and trees and subsequently identified the lichen species through DNA Barcoding. The project took six to seven months and involved background research, learning DNA Barcoding technology, sampling, and writing a 14-page research paper, among other tasks. Although the students had never done a project quite so extensive, when they saw their research yield conclusive results, they decided to submit it to the Siemens Competition.

It took a while … to process, to sink in. I was … kind of stunned, because I heard before that no one in the high school had gotten through, and there were a lot of really good projects here in the science research program.

At least one of the students plans to continue his research in Tenafly. He plans to analyze the lichen species in areas with known sulfur dioxide pollution to test the research's accuracy.

Wednesday, November 11, 2015

A mosquito on its way to Canada

Aedes japonicusis is a mosquito species native to Korea, Japan, Taiwan, southern China and Russia. It is not considered an important disease vector although there is concern that this species may become a pest problem or be involved in the transmission of North American arboviruses such as West Nile virus, La Crosse virus, as well as Japanese B. The mosquito was first reported in the Unites States in 1998 and since then it spread into 30 states and was occasionally sighted in Ontario, Canada. It is also widespread in Europe.

The success of the invasion of Aedes japonicus is has been due to a number of factors including its ability to withstand long distance dispersal and winter temperatures in our regions, as well as its high tolerance to organic concentrations in various forms of natural and artificial containers.

A team of researchers from Simon Fraser University and Culex Environmental, found Aedes japonicus for the first time in Western Canada and just published on their find. Several specimens were obtained in suburbs of Vancouver. 

Species identification was done based on morphology of reared adults as specimens were obtained in several larval stages. Although I don't doubt the accuracy of the identifications of the authors I wonder why molecular methods of species identification such as DNA Barcoding are not already used in such cases. BOLD has more than 80 reference sequences for Aedes japonicus alone. It would safe the time and effort used to rear the larvae to adulthood and given all labour and procedures involved it would likely cost about the same. Furthermore, it would allow more widespread testing to survey the extent of an invasion and to monitor its spread. The workforce that can reliable identify Aedes species based on morphology is certainly limited.

Tuesday, November 10, 2015

Internet Archive to The Commons

Image from "The Lepidoptera of the British Islands...."
Yesterday I received a very interesting email from the Annelida newsletter system. I made me aware of the huge amount of information that is available through Flickr's Internet Archive. Over a while they were populating this area with images of book pages. Here a little bit of background from their website:

The Internet Archive is best known for its historical library of the web, preserving more than 400 billion web pages dating back to 1996. Yet, its 19 petabytes include more than 600 million pages of digitized texts dating back more than 500 years. What would it look like if those 600 million pages could be “read” completely differently? What if every illustration, drawing, chart, map, or photograph became an entry point, allowing one to navigate the world’s books not as paragraphs of text, but as a visual tapestry of our lives? How would we learn and explore knowledge differently? Those were the questions that launched a project to catalog the imagery of half a millennium of books.

A Yahoo research fellow at Georgetown University, Kalev Leetaru, extracted over 14 million images from 2 million Internet Archive public domain eBooks that span over 5 centuries of content, compiling more than 14 million high resolution images spanning nearly every topic imaginable. Each image includes detailed descriptions, including the subject tags of the book it came from and the text immediately surrounding it on the page. The latter is especially powerful, as it allows to keyword search 500 years of images, instantly accessing particular topics or themes. Searching for love yields a myriad images of cherubs and courtship, while mortis (death) offers a glimpse into the early modern period’s fascination with the subject. A search for bird offers a vividly colorful showcase of the world’s bird species, while searching for telephone traces the invention’s history from its introduction as an electric novelty to its widespread adoption.

It is very easy to search through this vast amount of data. Here are some links to give you an idea:

As you can see the search can be easily narrowed down through modification of the hyperlink (after the "text=" section). 

Happy browsing.

h/t Geoff Read

Monday, November 9, 2015

Chinese Amphibians

Since 2013, Cold Code, the initiative to barcode all amphibians and reptiles is working to assemble a DNA Barcode reference library. Cold Code is being coordinated out of the Kunming Institute of Zoology (KIZ), Chinese Academy of Sciences. To assure success, the project received start up funding. As a result, Cold Code offers to sequence the first 10 specimens of a species at no cost to an investigator but those requesting the service must submit relevant voucher data associated with the tissue samples. These data include but are not limited to species identification, collecting information locality (with GPS data), voucher specimen number (including image), collectors and steward of the data. 

The colleagues in China now presented some of their progress on amphibian barcoding. A new website, developed by the Kunming Institute of Zoology, provides information on Chinese amphibian species for herpetologists and the general public alike. As you can tell from the screenshot the site is in Chinese but Google translate does a fairly decent job to allow you to explore the site. 

The site currently holds 302 out of the 429 species of Chinese amphibians and according to the press releases all of them have a DNA Barcode. I am not sure if all these sequences are also on public databases such as BOLD or GenBank. The site has an ID engine (based on the BLAST algorithm) available but I wasn't able to access the reference library.

This is great progress for Cold Code and the website shows some very interesting creatures with detailed information on them.

Friday, November 6, 2015

Three steps for better protected areas

Achieving CBD's goals are imperative for nature and humanity, as people depend on biodiversity for important and valuable services. The scientific community now must step up and actively help governments identify what is need for their future protected area estates so they can achieve great conservation outcomes.

The Convention on Biological Diversity and its 193 signatory nations established 20 Aichi Biodiversity Targets organized under five strategic goals. Aichi Target 11 says: By 2020, at least 17 per cent of terrestrial and inland water, and 10 per cent of coastal and marine areas, especially areas of particular importance for biodiversity and ecosystem services, are conserved through effectively and equitably managed, ecologically representative and well connected systems of protected areas and other effective area-based conservation measures, and integrated into the wider landscapes and seascapes.

We are half way into this ten year plan, and progress towards the targets has been made, with 15.4% of the world’s terrestrial area and 8.4% of the marine realm covered by a Protected Area (PA) under national jurisdiction. Yet it is widely accepted that the overall PA estate is inefficient because PAs: are often poorly-located as well as poorly-managed; fail to capture important elements, functions and services of biodiversity; and, are failing to address continuing pressures such as outright habitat loss and resource exploitation, due to corruption, poor governance, or insufficient financial resources.

An international group of researchers has developed a three-point plan to ensure the world's protected areas meet these targets as they recognize that part of the current failure of the protected areas to stop the decline of biodiversity is partly to do with the lack of science available. The colleagues offer strategic guidance on the types of science needed to be conducted so PAs can be placed and managed in ways that support the overall goal to avert biodiversity loss. The three points of their solution are:

  1. Establish ecologically sensible protected area targets to help prioritize important biodiversity areas and achieve ecological representation.
  2. Identify clear, comparable performance metrics of ecological effectiveness so conservationists can assess progress toward the targets.
  3. Identify metrics and report on the contribution of "other effective area-based conservation measures (OECMs) make toward the target.