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.

Thursday, November 5, 2015

You better know what bit you

King Cobra (Ophiophagus hannah)
Bites from venomous snakes are common in many parts of the world and a serious unresolved health problem to millions of people living in South and Southeast Asia, as well as Africa and Latin America. Although there are no reliable numbers at the global scale, it has been estimated that at least 421,000 cases of venom snakebites with up to 94,000 deaths occur worldwide each year. However, experts warn that these figures likely underestimate the real problem, which is believed to affect several million people bitten by venomous snakes annually and hundreds of thousands who die or survive disabled, suffering from amputation or deformed limbs as a result of unavailable or delayed treatment.

People bitten by snakes often do not seek treatment at a medical facility, and if they do, the vast majority don't take the snake with them although it is often killed. Of course they also can't identify the species that actually bit them. However, knowing the species of snake is critical to determining the best course of treatment. And even if the victims do everything right, the clinical personal does not necessarily have the expertise to identify the snake species.

Researchers from Thailand have now build a first DNA Barcode reference library for venomous snakes and one non-venomous snake (Python bivittatus bivittatus) found in Thailand. Based on their results they also developed species-specific multiplex PCR markers to allow for rapid delimitation of
eight groups of venomous snakes for which the Thai Red Cross keeps antivenom for clinical use. This assay could easily be applied to venom and saliva samples. If venom could be assigned to a particular species, doctors could quickly give anti-venom instead of waiting for clinical signs of poisoning, as it is current practice. This would also accelerate the transfer of patients to referral hospitals with intensive care units able to ensure adequate respiratory support. Such a test would be easy to administer in rural healthcare settings with limited resources.

This is a promising development in the search for an efficient means of examining snakebites, which could ensure the application of appropriate antivenom therapy. However, improvements in the sensitivity of markers, the limitation of locally restricted markers, and protocols for DNA isolation from a remnant swap are still required in order to produce an optimal and practical procedure for the delimitation of snake species.

Wednesday, November 4, 2015

Maine Barcode of Life Project

I have talked about this repeatedly - DNA Barcoding lends itself to education at various levels. Not only is the concept relatively simple to understand, but is also multidisciplinary and modular by nature. Schools, colleges and universities start embracing it more and more although the latter could do more for my taste. Very often it is independent organisations that take up the idea and offer it to students and/or teachers. A good example are our friends from Coastal Marine Biolabs in Ventura, California. 

Another rather new organisation that offers inroads to STEM (Science, Technology, Engineering and Math) education is iXplore, an independent, nonprofit organization with the goal to encourage students to pursue STEM degrees, to promote STEM awareness in the state of Maine, thereby expanding the skilled workforce supporting STEM-dependent business sectors.

Program participants contribute to the Maine Barcode of Life project using DNA Barcoding while working in a college biochemistry lab at the University of New England. Participants are introduced to molecular biology, ecology, and evolution concepts and develop lab skills such as centrifugation, electrophoresis, and polymerase chain reaction. Students learn to use computational biology and bioinformatics to analyze their DNA barcodes with tools embedded in the BOLD-Student Data Portal

This is a great trend which I hope will continue and include more fields of science. The more hands on the better and a little fun doesn't hurt either.

All photos were 'stolen' from Deborah Landry who runs iXplore.

There's excitement in the air with the sense of doing real science! I never thought I would be able to do this in high school.

Tuesday, November 3, 2015

Bugs on the rooftop

Nut weevil (Curculio nucum)
As temperature increases we see a corresponding change in the insect community, specifically for the resource specialists -- the insects that feed on only one species of plant. Earlier studies have confirmed that specialist species also respond rapidly to destruction of their habitats, so we are dealing with a very sensitive group of animals.

A volunteer registration of insects for 18 consecutive years on the roof of the Natural History Museum of Denmark in Copenhagen has revealed local insect community turnover due to climate change. 1543 different species of moths and beetles and more than 250,000 individuals have been registered over 18 years of monitoring. That corresponds to 42 % of all the species of moths in Denmark and 12 % of the beetles. More interestingly, the insect community has changed significantly during that period.

The nut weevil (Curculio nucum) is an example of a resource specialist, feeding only on hazel. It lives further north in Europe than its close relative the acorn weevil (Curculio glandium), which feeds only on acorns. While the nut weevil was only registered during the first half of the study, the acorn weevil appeared in the last part of the study, suggesting that specialist species are moving northwards in Europe. Using the entire dataset, the study was able to confirm this trend and highlights the increased pressure on the most northern species, which may be 'squeezed out' of their range in the long term.

We are likely to lose some specialist species as they retreat north, but more new specialist species will arrive from the south. This trend is theoretically expected but extremely rare to confirm with observations across this many species. Insects are often over-looked and under prioritised for long term studies.

It was two employees of the Natural History Museum of Denmark with extensive entomological expertise who collected and identified all the insects. The monitoring took place every week from 1992 to 2009 through spring, summer and autumn using a light trap at the roof of the museum. What started out as a hobby based on scientific curiosity, ended up in an extensive faunal and climate change study.

Monday, November 2, 2015

Some like it hot, some not

The great puzzle has been why some species of moth and butterflies have been increasing and spreading, whilst others have declined in the last 40 years. Now we know that most of the differences arise because each species responds in a different way to the climate. Some like it hot, some like it cold.  Some like it hot in winter but not in summer. Some like it wet in spring, others dry in the autumn.

It has been repeatedly shown that organismal response to climate change varies greatly from species to species. Furthermore, this variability has been regarded as very complex due to the number of biotic interactions. This in turn has led to concerns that predictions of responses are inherently uncertain.

Variation among species is attributed to differing sensitivity to climate change, and also because species vary in how much the climate has changed for them (their ‘exposure’). Sensitivity is a measure of how much species’ numbers change as a result of year-to-year changes in the weather because each species is sensitive to different aspects of the climate, such as winter temperature or summer rainfall.  

Researchers from the UK have now analysed how the abundance and distribution of 155 species of British butterflies and moths have changed since the 1970s. Using data collected by thousands of volunteers through ‘citizen science’ schemes, responses to recent climate change were seen to vary greatly from species to species.

It turns out that these 155 different species of butterflies and moth have almost 155 different ‘opinions’ on how much the climate has changed, and whether it has got better or worse.  Climate change is causing massive alterations to our wildlife.

Results show that species such as the treble brown spot moth (Idaea trigeminata) and the speckled wood butterfly (Pararge aegeria) which are sensitive to climate, and for which the climate has improved the most, have experienced the greatest increases in their distribution size and abundance. Conversely, other species, such as the grizzled skipper butterfly (Pyrgus malvae), the September thorn moth (Ennomos erosaria) and the mouse moth (Amphipyra tragopoginis), have experienced deteriorating climates resulting in declines in abundance and distribution size.

Species are sensitive to different aspects of the climate, which results in species being exposed to different levels of climate change. Nearly two-thirds of the changes in abundance can be explained by these species-specific differences. This means that their responses to climate change may be more predictable than previously recognised.