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: