Thursday, February 28, 2013

Acacia conservation

The genus Acacia  is the most species rich vascular plant group in Australia, with over 1000 species. The genus dominates the many dry areas of the Australian continent. Quite a few of those species have conservation status in some regions of the continent mostly because they are endemic.

Some regions in Western Australia are currently the focus of extensive mining activity for iron ore. However, mineral exploration and extraction have the potential to significantly impact many narrow endemic species in the region. Government approval for such mining programs is conditional on the conservation management of rare flora therein as well as strategies for post mining ecological restoration. Rapid biodiversity assessment is an important component of this approval process  Many Acacia species will be particularly impacted by mining activities. Therefore, it is critical to assess the local diversity in an effective fashion.

Taxonomic characters:pods, flowers and leaves
Identification of acacias often requires a combination of pods, flowers and leaves. Diagnostic taxonomic characters are often only found in reproductive material, which can be difficult to collect in dry regions where reproduction is restricted to years with sufficient rainfall. Even when reproductive material is available, morphological differences between taxa are often subtle.

A group of Australian researchers investigated sequence variation of the extant Acacia species at a mine site at plant DNA barcoding and other plastid loci, and used their findings to identify an ambiguously labelled seed collection. They tested both standard plant DNA Barcodes (matK and rbcL) and some other chloroplast regions (rpl32-trnL, psbA-trnH, trnL-F and trnK). matK was able to resolve six of the eleven study species but proved to be difficult to amplify and sequence. rbcL on the other hand was straightforward to recover and align, but species resolution was poor. As a consequence the authors recommend using both formal barcoding regions supplemented with data from other plastid regions, particularly rpl32-trnL, for DNA Barcoding Acacia.

Wednesday, February 27, 2013

eBOL Launch

This is our week of educational activities. On Tuesday we started with our School Malaise Program
The BIOBus at King George Public School in Guelph
and we've visited three elementary schools so far. Only 57 more to go! Check out Twitter or Facebook for more info and pictures like the one on the right.

Today is the day for the next big news:
Together with our friends from Coastal Marine Biolabs in Ventura, CA and the crew from Spongelab we (BIO and BOLD) launched eBOL a new community tool developed for educators who want to use DNA Barcoding as a classroom tool. Here the official press release:

Developed in partnership with educators, bioinformaticians, researchers, and science media experts, the eBOL Community Web Portal integrates new digital resources to bridge the biodiversity knowledge gap and advance DNA barcoding as an interdisciplinary teaching and learning tool.

"DNA barcoding has stimulated a great deal of interest and excitement from high school science teachers and university instructors who struggle to bring authentic research experiences into their science labs," said Linda Santschi , Scientific Co-Director of the California-based Coastal Marine Biolabs.  The ability of DNA barcoding to bind different life science disciplines within a single scientific workflow is extremely attractive to educators who are frustrated with prescriptive and outmoded lab experiences. "Through eBOL, we have a unique opportunity to not only heighten student awareness of this powerful new technology and how it works, but to develop it as a model to innovate life science education." 

At the center of this open-access resource is a customized student interface to the world-class Barcode of Life Data Systems (BOLD), an enterprise-scale informatics platform that forms the framework for DNA Barcoding technology.  "For the first time since the launch of the landmark International Barcode of Life (iBOL) project, students around the world have a direct link to the biodiversity genomics community," said Sujeevan Ratnasingham, the Director of Informatics at the Biodiversity Institute of Ontario (BIO).  Through the BOLD Student Data Portal (BOLD-SDP), students can utilize a centralized suite of sophisticated informatics tools that enable them to manage, analyze, and share various forms of barcode data with each other and the global iBOL community.  

In addition to BOLD-SDP, the eBOL website provides a gateway to new mobile computing technology for collecting barcode data in the field, and an extensive and indefinitely expandable library of high quality digital learning assets maintained by Spongelab, an award-winning science media and communications group based in Toronto. According to Dirk Steinke , the Director of Education and Outreach at BIO, the establishment of the eBOL website equips educators with the information and tools needed to seamlessly bridge DNA barcoding and education in classrooms worldwide. It also encourages the formation of a diverse and broadly inclusive community committed to revitalizing life science education.  "We envision a future where students working in school and university labs around the world can make lasting contributions to iBOL and meaningfully explore the value of DNA barcoding for addressing a variety of important real-world problems." 

Tuesday, February 26, 2013

DNA Barcoding on CNN

That one kept me busy yesterday. Five hours work resulting in 3 minutes. You gotta love TV

Friday, February 22, 2013

Seafood mislabeled again and again

Roughly one third of the seafood sales in the US are mislabeled. A new study by Oceana is making headlines since yesterday. Again, DNA Barcoding was the technique used to show that cheaper farmed fish are often substituted for wild species, such as tilapia sold as red snapper and Atlantic farmed salmon sold as wild or king salmon. Who wants to go to a Sushi restaurant in one of the regions tested if in 74% of the cases you don't get what you pay for?

Overview of rates of seafood mislabeling  in US states and metropolitan regions

Our lab here at BIO has done most of the leg work for these studies and stories (also for this particular one) and since 2008 we repeatedly showed that especially in the seafood business mislabeling is rampant, not only in the US. Did anything happen to change this? Not really.

One big step forward in the US was the adoption of DNA Barcoding as regulatory protocol by the Food and Drug Administration (FDA). In addition the global initiative to build a library of DNA Barcodes for all fish FishBOL has assembled reference barcodes for most if not all currently commercially important species. Actually the total number of species almost surpasses the 10,000 mark. In other words, the tools to test are in place. However, this doesn't help any consumer if less than 1% of the imported and landed fish is actually tested as it is the case in the US.

Other countries (including Canada) are not even at this point and this form of fraud is not limited to the US. There have been studies in Europe that all came up with similar numbers. I wouldn't be surprised if globally we are looking at a mislabeling rate of 30-40%. This rate will likely increase as demand for particular species won't diminish although the stocks of many fishes are depleted.

I found some reasonable suggestions for every consumer in an article in the Huff Post:

Consumers can also take steps on their own to stop seafood fraud. They should start by asking questions -- what kind of fish are they being served, is it wild or farmed-raised, and where and how was it caught. Buy seafood that is traceable and support the voluntary programs that are already in place. Check the price. If it seems too good to be true, it probably is. And finally, when possible, purchase the whole fish. Species are easier to identify this way and seafood fraud is much harder to pull off if the fish is not already filleted and processed.

The only thing I would like to add at this point is to demand better regulation from our goverments. As taxpayers we have all the rights to ask for better (only the US FDA is officially using DNA Barcoding at this time) and broader testing (less than 1% in the US - give me a break). Especially given that some of the substitutions that are happening actually represent health risks such as 84% of white tuna samples in the Oceana study were actually escolar, which can cause digestive problems.

It took 10 years for the initially controversial idea of DNA Barcoding to reach a point where it can really make a huge difference in all our lives. Let's hope this chance will be used wisely.

Thursday, February 21, 2013

School Malaise Trap Program

We are currently in the last phase to prepare for a new education and outreach project:

Next Tuesday we will start to visit 60 schools in Southern Ontario and team up with grade 6 and grade 12 students to explore the insect diversity in their schoolyards through DNA Barcoding.

Each school will get a visit by our BIObus, an RV converted into a field laboratory, with a team that will introduce students to some methods of fieldwork. We will provide insights into biodiversity research and present DNA Barcoding. Teacher will be supplied with a comprehensive lesson plan designed to fit the respective curricula. 

But that's not all. Each class will put up a so-called Malaise trap to collect insects in the schoolyard over a two-week period in April. 

A malaise trap is a trap for flying insects, particularly flies, wasps, and true bugs. It is usually placed in a natural flyway where it can easily collect hundreds of insects in a week thereby providing a very detailed understanding of local biodiversity. Invented by the Swedish entomologist RenĂ© Malaise, it resembles a black and white tent with a mesh panel along its central axis. When insects encounter the panel, most will naturally go up towards the white coloured roof in an attempt to pass the obstacle. The insects are directed to the top of the trap where they are caught in a collection bottle. 

Here is how to build up one (our detailed instruction video for the classes):

Once the two weeks are over all samples will be analyzed at our facility and each class will receive a detailed report on species found but also comparisons between all 60 locations.

I'll be on the bus for a couple of (not all) trips over the next 6 weeks. I am sure there will be plenty to blog about. In any event a great opportunity to bring our research into the classrooms and allow the kids to participate in ongoing research.

Wednesday, February 20, 2013


Recently I have started using figshare to share some figures I've created a while back and that perhaps otherwise would have never seen the light of day. I am certainly not the only one having stuff in the drawer because we never got to finish a manuscript or get to a few more experiments. Another phenomenon playing into this is also widespread and has been named the file drawer effect. Many studies in a given area of research may have been conducted but never reported, because we all have the tendency to not publish negative or inconclusive results. 

There is an open source solution to this available and it doesn't cost you anything aside from a couple of minutes to upload your data. figshare allows researchers to publish research outputs in an easily citable, sharable and discoverable manner. All file formats can be published, including videos and datasets. There is no peer review process, and researchers are actually encouraged to publish null results, avoiding the file drawer effect. figshare uses creative commons licensing and provides you with a DOI and a QR code for every file you've uploaded. Categories and tagging support easy access as well

I have just started using it and I really like this way of sharing results openly. Not only is it a home for all the used (of course the ones published should be up as well) and unused figures but also a great resource when it comes to preparing lectures, courses, and talks. There are some great resources for teachers out there but not as many for university educators.

And most importantly it is real open access. In case you haven't heard of figshare, please check it out and start sharing.

Tuesday, February 19, 2013

New crustaceans

Colour photographs of the Lauriea species in the study
(credit G. Paulay & T.Y. Chan)
A large number of specimens of crustaceans of the genus Lauriea, along with colour images of some specimens, have been collected by numerous expeditions over the past decades in the Indian and Pacific Oceans. Two researchers from the Centre for Advanced Studies of Blanes and the University of Barcelona examined all the material that came from recent expeditions to Madagascar, New Caledonia, Vanuatu, the Philippines and French Polynesia.

Using morphological and molecular data (DNA Barcodes and 16S rRNA) they have discovered five new species of crustaceans belonging to the genus Lauriea (family Galatheidae). They are genetically different but morphologically very similar. The authors also described a new genus, named Triodonthea

The new species can only be differentiated by their molecular data, colour patterns and a few subtle morphological differences. The molecular and the colour information provide the most consistent differences, whereas the morphological characters can be variable and are therefore difficult to use. These small critters (between 1.5 and 3 cm length) belong to the so-called Squat lobsters which are usually flattened with their long tails held curled beneath the thorax. The majority of squat lobsters are benthic, spending their lives on the sea-floor. Flesh from the larger species is often commercially sold in restaurants. There is also demand for squat lobster meat as feed in fish and shrimp farms. This is in part because they contain astaxanthin, a red carotenoid pigment that helps to colour the meat of farmed fish.

Monday, February 18, 2013

Marine Klee-diagrams (3)

This is the last part of my little experiment on open access sharing via blog. The data and applications presented were part of a draft publication that needed a bit more in order to be submitted but there was no time to finish it. On the other hand I thought it should be shared with a larger audience instead of hiding it on my hard disk. So, here it is - the last third of a manuscript that was never fully completed nor submitted. I rearranged and edited a few sections but that's all.

and now ... genetic variation

The indicator vector method has been only applied to COI barcode data so far. Its utility with respect to other genes or for comparison of several gene diversity patters of a set of organisms hasn’t been tested yet. Here I show two comparisons of fish sequence data obtained from full mtDNA sequences on GenBank. All analyses were done with different mtDNA sequences of the same individuals of 486 species representing 80% of all extant fish families. 

Klee diagrams for 486fish species using indicator vectors for full length COI, COI barcode region ,and COI mini-barcodes (Meusnier et al. 2008). Data were retrieved from full mtDNA genomes atthe NCBI Genome database.

The figure above represents a comparison of the full length COI sequence, the standard COI barcode region, and the mini-barcode region proposed for archival sequences. It demonstrates the gradual loss of discontinuities necessary for separation into species. However, especially the differences between the full length COI and the DNA Barcoding region are not very pronounced thereby confirming the utility of COI Barcodes in fishes that has been shown in so many studies.

It has also been shown that several important attributes of complete mitochondrial genomes can be predicted with high accuracy from the DNA barcode sequences alone. These attributes include average nucleotide composition, patterns of strand asymmetry, GC content, and the high frequency of codons that encode hydrophobic amino acids. Therefore, DNA Barcodes, or other short sequences sampled from a wide taxonomic range, can give a meaningful overview of variations in genome composition long before complete genome sequences become available for many of the sampled taxa.

In an attempt to confirm these findings across a wide range of fish species and to further test the capabilities of the indicator vector method I conducted a parallel analysis of 6 representative mtDNA genes (ATPase 6, Cytochrome b, Cytochrome Oxidase I, II, III, NADH dehydrogenase I) imposing an identical order of sequences to all data subsets. They were organized based on the topology of a Maximum Likelihood tree generated in RAxML with a concatenated dataset of all mtDNA sequences obtained. A partitioned maximum likelihood analysis was performed with the GTRMIX option. The resulting topology was used to re-order all single gene data sets.

Klee diagrams for 486fish species using indicator vectors for Cytochrome Oxidase I (COI), II (COII),III (COIII), Cytochrome b (Cytb), NADH dehydrogenase 1 (ND1), and  ATPase 6 ,. Data were retrieved from fullmtDNA genomes at the NCBI Genome database.

All Klee-diagrams retrieved were strikingly similar in appearance indicating similar signals from all datasets.  Blocks of high correlation on the diagonal that are reflecting affinity among species are visible in all cases. COI and Cytb produced relatively smooth mapping, with maximum correlation among neighboring species, and decorrelation among more distant species. Given the broad sampling across all fishes the latter occurs much more frequent. 

There is increasing evidence that within the nuclear genome, selection works at a fine scale—gene by gene—rather than on a genome-wide basis. Because the mitochondrial genome is inherited as a single molecule, mutational biases or selective events would likely act on it as a whole, providing a basis for the overall similarity of the false-color maps of all used mtDNA coding genes. This means that any subset of the mitochondrial genome could be used as a sentinel sequence that provides rapid insights into nucleotide usage and composition.