Wednesday, September 30, 2015

Wonderful arthropods

After my rant yesterday, today on a much lighter note. The omnipresence of the internet might have its good and bad sides but one really good one is the fact that everybody has access to a myriad of wonderful images of live on our planet. The world is full of talented photographers that are able to capture the beauty of living things and nature itself. Not long ago I introduced you to Alexander Semonov and his beautiful images of marine life. Today I will add a few more names to the list.

The first is a colleague working as collections technician at our institute, Valérie Lévesque-Beaudin. Valérie is an entomologist with a passion for macro photography and of course most of her images show her favorite organisms - arthropods. I selected one photo (above) I particular like but have a look at her Flickr presence for a much larger selection.

Number two is Thomas Shahan, who was nicely introduced in an article by the Smithsonian magazine and on TV. Just look at the moth I grabbed from his Flickr site.

Number three used to work for BIO as well. His name is Jay Cossey and I had the pleasure to take him to an expedition to the Great Barrier Reef a number of years ago. His insect photo's are stunning and his work was recognized before, e.g. he did all 24 images for the first ever National Geographic Butterfly Calendar. I choose an image showing him in front of one of his photos. I believe this photo was taking for a university publication way back then.

The last of my 'photo heroes' today is Sam Harris who is a Graduate Student (Ph. D. in Biology) and Teaching/Research Assistant at the University of Tulsa. At least that's what his Flickr profile said where I found some awesome spider portraits.

There are of course many more talents out there and I promise to post more in the future. In case you know of any please let me know or add a link or a name in the comments.

Tuesday, September 29, 2015

A rare rant

Unlike many other blogs I usually try to stay out of politics in general. Criticism is usually scientifically founded and perhaps the direct outcome of some new findings I came across. The DNA Barcoding blog is not a political venue per se which is why you usually don't read a lot about my (very low) opinion of climate-change deniers, creationists (including intelligent design followers), violent extremists of all sorts, racists, misogynists, and so on.

That being said, today I will make an exception and by the end of the post you might understand why.

Those of you who are doing molecular phylogenetic analysis might have heard or even used the versatile software Treefinder. It is one of many different programs out there, has been used by a part of the community, and is free of charge. Treefinder was developed by Gangolf Jobb, a researcher from Germany. Over the years Gangolf Jobb has repeatedly complained about the fact that he was never paid for the development of the program and many other things. This was one of the reasons why I after a brief test decided not to use the program as there are so many equally free alternatives out there which are happily shared by colleagues that are not paid for that either. Let's face it, our research community has no money for software to begin with. 

However, all that wouldn't be worth a single line of a post or even a tweet. It is what Gangolf Jobb did next. Effective October 1st he revoked licenses for users that live in those EU countries that host most of the refugees that are currently fleeing to Europe. Do you want to know why? Read this:

The reason: I am no longer willing to support with my work the political system in Europe and Germany, of which the science system is part. There is no genuine democracy, and I disagree with almost all of the policies. In particular, I disagree with immigration policy. Immigration to my country harms me, it harms my family, it harms my people. Whoever invites or welcomes immigrants to Europe and Germany is my enemy. Immigration is the huge corporations' interest, not peoples' interest. I am not against helping refugees, but they would have to be kept strictly separated from us Europeans, for some limited time only until they return home, and not being integrated here as cheap workers and additional consumers. Immigration unnecessarily defers the collapse of capitalism, its final crisis. The earlier the system crashes, the more damage can be avoided. Possibly a civil war in Europe. Not to mention the loss of our European genetic and cultural heritage.

This is probably just a provocation of a desperate attention seeker but for that it goes way too far. As a German I am sick of reading rehashed Nazi propaganda especially when it comes from home. I am really glad that the vast majority in my home country thinks fundamentally different and many many Germans demonstrated their compassion and went out of their way to help. However, people like Gangolf Jobb are a shame, not only for Germany, but in this particular case for the scientific community at large and the evolutionary biology community in particular. Do we really have to listen to this scientist's complaints about the loss of European genetic heritage through immigration of refugees? This is simply disgusting and nauseating. 

There are currently millions of people that somewhere in the world literally run and swim for their lives trying to reach a place somewhere safe. It is bad enough to see how reluctant and sometimes dismissive political leaders react these days, but we certainly don't need to listen to the old propaganda of fear and hate. One parental lineage of my family consists of refugees from Eastern Prussia fleeing to the West in 1945. Not only did they have to leave home as a result from a war caused by the very same wrong-headed ideology that spoke of the protection of genetic and cultural heritage, but they also had to run for their lives knowing that they might never be able to go back. Such people need help and compassion, not refusal and hate.

And they certainly do not need Gangolf Jobb's 'wisdom'. 

Monday, September 28, 2015

Lager beer diversity

Research is sometimes triggered by the strangest things. Some newly published research e.g. originated during a Friday evening beer tasting at a lab of the University of  Leuven, Belgium. On a regular basis students taste and discuss five or six related beers. 

One night, we tasted six Pilsner-type beers, and someone commented on how similar they were, much more so than beers of other types.

Unlike ales, lager beers (such as the Pilsner-type) differ little in flavor. Lager beers are fermented with Saccharomyces pastorianus, which is a hybrid cross of Saccharomyces cerevisiae and Saccharomyces eubayanus, at temperatures generally between 8 - 15 C. They also have a lower alcohol content, 4 - 5.5 vol%. Ales are fermented by Saccharomyces cerevisiae, at higher temperatures- usually between 15 - 25 C., and they tend to be stronger than lagers.

The researchers didn't leave it at that and did what every good scientist does. They developed some hypotheses and put them to the test. Their assumption was that if they could create more crosses between Saccharomyces cerevisiae and Saccharomyces eubayanus, they would perhaps produce a set of more diverse lager yeasts, which in turn could yield more diverse lager beers. Problem is that both yeast species are very different from each other and the researchers had to do a lot to optimize growing conditions, hoping to facilitate mating between the yeasts. To this end, they experimented with different temperatures and growing media.

We were able to get some serious sexual action between our yeasts, which resulted in hundreds of new lager yeast strain. 

But of 31 new strains that they tested in small scale beer fermentations, only ten performed reasonably well in terms of speed of fermentation, and flavor. Some were really bad according to the testers. The best four were subsequently tested in full scale fermentation. 

Two were magnificent,they fermented more quickly than the commercially used reference lager yeast that we compared them to, and they produced really nice flavors.

We found that the different lager yeasts that we created showed very different aroma profiles compared to today’s commercially available lager yeasts. This means that it now becomes possible to make lager beers that, like ale beers, are more different from each other, and this without the need to extensively change the production process.

That's what I would call curiosity-driven science. 

Saturday, September 26, 2015

School DNA Barcodes published

Participants of the School Malaise Trap program told us repeatedly that perhaps the most important aspect of the project, the one that students regard as particularly exciting, is the fact that they take part in the creation of a valuable public and scientific resource. They know their work will have a lasting impact.

In case there are people that had any doubts that school data would actually be used in science let me point you to a new paper published just yesterday. Research colleagues in Norway analysed data of the chironomid genus Tanytarsus

We explore the quality of DNA barcodes to delimit species in the diverse chironomid genus Tanytarsus (Diptera: Chironomidae) by using different analytical tools. The genus Tanytarsus is the most species-rich taxon of tribe Tanytarsini (Diptera: Chironomidae) with more than 400 species worldwide, some of which can be notoriously difficult to identify to species-level using morphology. Our dataset, based on sequences generated from own material and publicly available data in BOLD, consist of 2790 DNA barcodes with a fragment length of at least 500 base pairs. A neighbor joining tree of this dataset comprises 131 well separated clusters representing 121 morphological species of Tanytarsus: 77 named, 16 unnamed and 28 unidentified theoretical species. 

Chironomids are notoriously common in Malaise trap collections. It comes to no surprise that a global search for data records will reveal some school samples. However, to my knowledge this is the first time such a result makes it into a research paper. In total the study includes 47 samples from Canadian schools. And here we go - congratulations to the following schools. Your data have just made it into PLoS ONE.

  • Belfountain Public School
  • Centennial CVI, Guelph
  • John F. Ross C.V.I., Guelph
  • Hagersville Elementary School
  • Listowel Central Public School
  • Craig Kielburger Secondary School, Milton
  • Woodcrest Public School, Oshawa
  • Owen Sound C.V.I.
  • Mornington Central School, Perth East
  • Little Falls Public School, St. Marys
  • St. Marys District C.V.I.
  • Sacred Heart School, Teeswater
  • Walpole Island Elementary School, Wallaceburg
  • Donald A. Wilson Secondary School, Whitby

Friday, September 25, 2015

From the inbox: eDNA Postdoc

Great eDNA PostDoc Position: 

The Center for Ocean Solutions is seeking a Postdoctoral Scholar / Early Career Fellow (ECF) responsible for leading the environmental DNA (eDNA) aspects of the Marine Biodiversity Observing Network (MBON) project at the Center for Ocean Solutions. The MBON project is a collaborative project between the Center for Ocean Solutions, MBARI, NOAA and the University of Florida, funded by NASA and NOAA focusing on the Monterey Bay and Florida Keys National Marine Sanctuaries as sentinel sites for a demonstration marine biodiversity observing network. The work is aimed at integrating data from physical, chemical and biological monitoring methods with cutting-edge eDNA technology to track ocean biodiversity. The eDNA work of the MBON project led by Ali Boehm at Stanford University and the Center for Ocean Solutions aims to develop novel genetic methods to monitor fishes and marine mammals in marine environments. We seek an individual with a strong background in molecular biology and environmental genomics who also is interested in linking science to decision making. Click here or here to apply.

Thursday, September 24, 2015

Strontium ratios in ecology research

Strontium ratios in rocks vary depending on the type of rock and the rock's age. The continental-scale water model previously developed by researchers at the University of Utah, uses bedrock geology and all major river systems and drainages to predict strontium isotope ratios (the ratio of strontium 87 to strontium 86) in surface waters. These applications of strontium isotope analysis are focused on quantifying weathering rates for minerals and rocks, and the sources and fates of strontium in rivers.

Tracking strontium isotope ratios is a valuable tool beyond the science described above. The heavy metal strontium can be found in most organic substances such as bones, teeth, soils and plant tissues. As a result, strontium isotope ratios are used in fields including forensics research, animal poaching investigations, and even tracking where marijuana plants came from in drug busts. 

Research, led by colleagues at the University of Cincinnati, used the above mentioned water model to compare predicted strontium isotope ratios in surface water, soil, vegetation, fish and mammal skeletal tissues from a massive collection of data  across the U.S., excluding Alaska and Hawaii. 

Because the ratio of strontium 87 to strontium 86 in water, soil, vegetation and animal tissues predominantly reflect local geology, they can be used to distinguish geologically distinct regions as well as identify highly mobile populations. We tested how accurate the model was at predicting strontium ratios not just in water, but in additional materials relevant to ecological and paleoecological research.

Although strontium isotope analysis related to biological research is certainly on the rise, the expense in terms of ground mapping has so far been prohibitive. 

It's a really powerful system, but in order to get an idea of where elephant tusks confiscated in Kenya came from, for example, investigators would have to track the strontium signals throughout the country or potentially all over East Africa. Models like the one we tested could make it possible to quickly get a good idea of where that animal was originally from.

The researchers say the water model provides a readily available source of background data for predicting strontium ratios for biologically relevant materials in regions where empirical data are lacking. The availability of increasingly high-quality modeled strontium data will dramatically expand the accessibility of this geochemical tool to ecological applications.

Wednesday, September 23, 2015

Slow nanopore sequencing

In nanopore sequencing, DNA passes through a tiny pore in a membrane, much like a thread goes through a needle. The pore also contains an electrical current. As each of the four nucleotides pass through the pore, they block the current in individual ways that can be used to identify them. The method is under development since the mid 1990s

Very recently this method caught the attention of the community including us barcoders as Oxford Nanopore allowed a limited number of users access to the MinION device through their MinION Access Programme. A couple of talks (see here starting at about 32:00) at the last Barcode Conference demonstrated how close we might be to a miniature version of a handheld barcode scanner.

Although powerful, the method suffers from high speed: DNA goes through the pore too quickly to be read with best accuracy. Researchers at  the  Ecole Polytechnique Fédérale de Lausanne have now developed a way to overcome this problem by using a thick, viscous liquid that slows the passage of DNA by two to three orders of magnitude. 

The researchers developed a 0.7 nm thick film made of molybdenum disulfide (MoS2). This is different from the current solid state nanopores that are made with silicon compunds or graphene. DNA is a fairly sticky molecule and MoS2 is considerably less adhesive than graphene. The team then created a nanopore on a membrane, almost 3 nm wide.

The next step was to dissolve DNA in a thick liquid (room-temperature ionic liquid) that contained charged ions and whose molecular structure can be fine-tuned to change its viscosity. The results are quite promising: Our technique, which exploits the high viscosity of room-temperature ionic liquids, provides optimal single nucleotide translocation speeds for DNA sequencing, while maintaining a signal-to-noise ratio higher than 10.

The colleagues also predict that using high-end electronics and control of the viscosity gradient of the liquid could further optimize their system. With their approach they hope to create a cheaper DNA sequencing platform with a better output.

To conclude, we have demonstrated that single-nucleotide identification can be achieved in MoS2 nanopores by using a viscosity gradient to regulate the translocation speed. The viscosity gradient system can not only be used in standard ionic sensing experiments, but can be potentially combined with other schemes of nanopore sensing such as transverse current signal detection. The ultrahigh viscosity of ionic liquids results in reduced capture rates. Therefore, an optimal experimental configuration would capitalize on high-end electronics and the viscosity gradient system presented here with a suitable capture rate. We believe that combining ionic liquids and monolayer MoS2 nanopores, together with the readout of transverse current either using the tunnelling or FET modality, would meet all the necessary requirements for DNA strand-sequencing such as optimal time resolution and signal resolution. This could also be achieved in a platform that allows multiplexing, thereby reducing costs and enhancing signal statistics.

Tuesday, September 22, 2015

School Malaise is back

We're back for another run. Since yesterday 60 schools across Canada and even a few libraries in San Diego (can't wait to post some photos) are running Malaise Traps for two weeks. Here some impressions the groups send us over the last few days:

Friday, September 18, 2015

Australian bees

No doubt, bees are important pollinators of crops and native plants, but habitat loss and pesticides are proved to be causing a serious decline in their populations in Europe and the United States of America. Meanwhile, the conservation status of native Australian bees is largely unknown because solid baseline data are unavailable and about one third of the species are as yet unknown to science. Furthermore, identification of Australian bees is hampered by a lack of keys for about half of the named species.

With a new publication, bee specialists from the University of Adelaide and the South Australian Museum are trying to make Australian native bees more accessible to the scientific community. Their study introduces a public BOLD project, which will be built to contain the barcode sequences of the identified Australian native bees.

This paper launches an open access DNA barcoding project “AUSBS” under the Barcoding of Life Datasystems (BOLD). The aims of the project are to help scientists who lack the necessary morphological knowledge to identify known species using molecular markers, to aid native bee specialists with the recognition of species groups that morphologically are difficult to define, and, eventually, to assist with the recognition of new species among known species.

So far, the project includes 271 sequences of 120 species that were collected during the Bush Blitz surveys, Australia's largest nature discovery project. The researchers intend to build on the existing DNA database to cover as many as possible of the 750 Australian bee species. 

The paper also shows the utility of this project. After careful evaluation of the DNA sequence data and subsequent morphological comparison of the collected bees to museum type specimens, the colleagues recognized four new plasterer bee species in the genus Euhesma, which are described in the publication as well. Three of the species belong to the group of bees that specialize on the flowers of emu-bushes. These bees have evolved narrow faces and very long mouth parts to collect the nectar through a tight constriction at the base of the flowers. A similar evolution has been already observed in other groups of bees. The fourth species belongs to a different group within this large genus and has a normally shaped head.

In future, this database can help scientists who have access to molecular tools, but insufficient knowledge of bees, to identify known species. Yet, that is not the only use of the database. 

Bee taxonomists can access and use the molecular information to answer specific problems, for example, how certain species are related or whether or not a male and female belong to the same species. And combined with morphological information, the molecular database can help to identify new species.

Thursday, September 17, 2015

Africanized honey bees

The honey bee subspecies Apis mellifera scutellata, was introduced from southern Africa to Brazil in 1956 in an effort to breed honey bees better suited to the Neotropics. Swarms soon escaped containment and began to hybridize with European honey bees. The resulting hybrid offspring are known as "Africanized" honey bees. Africanized bees have since spread throughout much of the Western hemisphere, and arrived in the Southern United States in the mid-1980s.

Africanized bees are characterized by far greater defensiveness than European honey bees. They are more likely to attack a perceived threat and, when they do so, attack relentlessly and in larger numbers. Their hyper-defensive behavior has earned them the nickname "killer bees", an unfortunate misnomer which has caused the public to falsely believe that "killer bees" actually seek out and attack people for no reason other than sheer ferocity. That is of course total nonsense. 

Researchers from the University of California, San Diego used mitochondrial markers and morphometric analyses to determine the prevalence of Africanized honey bees in San Diego County and their current northward progress in California west of the Sierra Nevada crest. The current standard molecular method for identification is Restriction fragment length polymorphism (RFLP) analysis of the cytochrome b gene.

Some of the results were discussed in this TV interview with one of the authors, Josh Kohn:

In contrast to the statewide sample, honey bees throughout San Diego County were highly Africanized. Restriction analysis revealed that 64.8% of the 298 bees from San Diego County carried the African mitochondrion. 

The colleagues also found a single nucleotide polymorphism (SNP) at the DNA Barcode locus COI that distinguishes European and African mitotypes. In order to confirm its utility they took 401 DNA Barcode sequences from BOLD and mapped their occurrence data. Sequences with the putative African SNP are found only where they are known to occur (Africa, South and Central America and the lower U.S.) while European mitotypes are spread across continents. This won't change the fact that RFLP will remain method of choice as it is currently easier, cheaper and very reliable.

DNA Barcoding is becoming an increasingly popular method of assessing biodiversity used both in research and classroom contexts. Because honey bees are frequently collected during invertebrate biodiversity assessments that utilize DNA barcoding, the Barcode of Life Database will provide ongoing data on further spread of Africanized honey bees.

What a great way to use BOLD.

h/t Josh Kohn

Tuesday, September 15, 2015

Evolution of mountain endemism

Tropical mountains are hot spots of biodiversity and endemism but the evolutionary origins of their unique biotas are poorly understood. In varying degrees, local and regional extinction, long-distance colonization, and local recruitment may all contribute to the exceptional character of these communities. Also, it is debated whether mountain endemics mostly originate from local lowland taxa, or from lineages that reach the mountain by long-range dispersal from cool localities elsewhere. 

In order to answer these questions a Dutch-Malaysian scientific expedition collected tens of thousands of plants, animals and mushrooms at 37 locations on and around Mount Kinabalu in Sabah, Malaysian Borneo. The group used DNA Barcodes that in many cases were augmented with one or more other phylogenetically informative loci. 

The researchers showed that most of the species that occur on the mountain are younger than the mountain itself (6 Million years). They also demonstrated that the endemic biodiversity consists of two groups. Some of the unique species are immigrants from far away areas such as the Himalayas or China, most of which already adapted to a cool environment. Other endemic species evolved from local species that initially occurred at the foot of the mountain and gradually adapted to the cooler conditions in higher altitudes.

It is sometimes thought that tropical mountains are also locations where very old species survive. However, our research reveals that most of the species are young. New species evolve at the top the mountain, but these often evolve from species that already lived under such conditions. This is important for the protection of the endemic species. Our research reveals the extent to which species are able to evolve to keep up with climate change and this allows us to make predictions for the future.

Monday, September 14, 2015

Illegal trade of plants

For many people, plants simply fail to garner our concern and affection in the way that many animals do. While we increasingly hear about the illegal trade of elephant ivory, rhino horn and tiger parts, few people will have heard about the illegal trade in hundreds of plant species for horticulture and medicine. Yet, commercial illegal trade is an immediate threat to the conservation of hundreds, if not thousands, of plant species in our region.

Southeast Asia is a widely recognised centre of illegal wildlife trade - both as the source region for species ranging from seahorses to tigers, and as a global consumer of ivory carvings, wild pets, and traditional Chinese medicinal products.

While there are efforts to tackle illegal wildlife trade, the illegal trade of wild-collected ornamental plants, especially orchids still remains undocumented. 

Researchers of the National University of Singapore conducted extensive surveys of wildlife markets across Thailand, including border markets with Laos and Myanmar, and identified more than 400 species of ornamental plants in illegal trade, all of which are species widely prized by plant enthusiasts for their beauty, fragrance or rarity. Over 80% of these plants traded at the markets are wild orchids. Some of these were even listed in published literature as threatened. Several of the plant species the colleagues found in the markets are even new to science.

Interviews with traders at the markets revealed that most of them sourced the majority of their plants from neighbouring countries, despite domestic protections and restrictions on international orchid trade associated with the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). The observed trade volumes and richness of plants illegally traded during the survey also greatly exceeded government-reported trade volumes. Even worse, virtually none of the international trade observed during these field surveys are reflected in official databases, conservation action plans or government policies, even though the trade is occurring openly at public markets across the region.

In this case, we've simply turned a blind eye to plant trade and botanical conservation. This research highlights a common problem in the illegal wildlife trade - the invisibility of trades that have not been researched and are not recognised in official government databases.

Consequently, the researchers call for more attention to protect Southeast Asia's botanical diversity. In their paper, they highlighted the need for more monitoring and enforcement, as well as research to better understand the impact of trade on wild plant populations and everyone involved in illegal trade. They further call for increased awareness of botanical trade among the international initiatives to address wildlife trafficking.

Thursday, September 10, 2015

DNA from exuviae

Insect skins (exuviae) are of extracellular origin and shed during moulting. The skins do not contain cells or DNA themselves, but epithelial cells and other cell-based structures might accidentally attach as they are shed. This source of trace DNA can be sufficient for PCR amplification and sequencing of target genes and aid in species identification through DNA barcoding or association of unknown life stages.

Given the very low tissue content in exuviae it is rather challenging to extract sufficient quantities of DNA for further analysis. Even if one manages to end up with some DNA the question remains how pure it is and if it is actually the organism that shed the skin and not any contaminant especially from organisms that feed on the exuvia.   

Colleagues from Norway put this to the test and compared the performance of five different DNA extraction methods and direct PCR in isolation of genomic DNA from chironomid pupal exuviae in terms of cost, handling time, DNA quantity, PCR success, sequence success and ability to sequence target taxa. 

And the winner is:

The very low cost and handling time per sample, as well as, the lack of toxic chemicals makes QuickExtract™ the most time- and cost-efficient approach among the best performing methods tested. Cost and handling time might be of importance for studies requiring high volume DNA extraction and for instance rapid, cost-effective assembly of DNA barcodes. We would consider this extraction method for molecular studies that have large sample sizes and/or are limited in funding.

Wednesday, September 9, 2015

Flickr and BugGuide help determining species range

Credit: Michael Skvarla
Are you still wondering about the value of the involvement of amateur researchers (citizen scientists) for science in general? If you are a regular reader of this blog likely not. That is if I did a good job over the past years. In case you still wonder here another piece of evidence:

The social network image platform Flickr and the citizen science website BugGuide have helped scientists to expand the known range of a rarely collected wasp, native to the eastern United States. 

Orussus minutus, is a parasitic woodwasp that attacks the immature stages of longhorn and jewel beetles. This species was previously known from only 50 specimens mainly from the Northeast of the US a specimen found in Arkansas and encounters from Iowa, Minnesota, and Manitoba shared as photographs on Bugguide and Flickr significantly expand the known range of the species westward.

Spurred on by the find the researchers contacted colleagues who pointed them to a hundred unpublished specimens housed in the United States National Entomology Collection at the Smithsonian, many of which were collected as bycatch in surveys that targeted invasive species like emerald ash borer and Asian longhorned beetle. Many of those are also new state records.

We used two resources - photos on social media and bycatch from large trapping surveys - which are often underutilized and I was really happy we could work both of them into the paper. This work highlights their utility, as well as the importance of maintaining biological collections like the U.S. National Collection.

Friday, September 4, 2015

Conference addendum - Thank you, volunteers!

At the end of the 6th International Barcode of Life conference organizers and participants thanked everyone involved but there is never enough time to full show how much this help is appreciated. Here a re-post from our conference site that is BIO's shoutout to all the volunteers:

Now that the conference is over, we here at BIO have had some time to reflect on the events of that busy week. And one thing became extremely clear – we could not have done any of this without the support and dedication of our crew of volunteers and staff.

Putting together a conference as large as this one is no easy feat, and could not have been accomplished without the help of our tireless crew of volunteers. The staff of BIO offered their time, put on a blue shirt, and took on tasks far outside the norm to help make this conference happen. But the magic behind the scenes was not limited to those wearing blue – all the staff in collections, the lab, BIO admin, and BOLD deserve recognition for their efforts to support the 6th International Barcode of Life Conference.

Lead Volunteers

Vanessa BretonVanessa Breton
Lead Volunteer Coordinator
Viktor GazoViktor Gazo
Technical Support Lead

Volunteer Team

Emily BerzitisEmily Berzitis
Volunteer Coordinator
Vanessa BouwerVanessa Bouwer
Administrative Support
Liza FritzscheLiza Fritzsche
Prize Coordinator
Chris HoChris Ho
Volunteer Guide
Susana Miranda RomoSusana Miranda Romo
Volunteer Coordinator
Claudia SteinkeClaudia Steinke
Volunteer Guide


Graham AnsellMaryam FatahiJaclyn McKeownJesse Sills-Gilligan

Tour Coordinators

Thanushi EagalleKellyn HawleyRenee LabbeeCarole Ann Lacroix
Suresh NaikKate PerezCrystal Sobel Jayme Sones

Additional Volunteers

Tim BartleyNick JefferyKevin MoreyRachel Smith
Danielle BourqueJessica JohannsonDerek MorningstarAlexandra Stoneham
Gina CaprettaTony KessLuke NoletMichaela Strüder-Kypke
Michelle D’SouzaOlga KiseliovaMatthew PalominoAisha Tahir
Forest DussaultLisa LedgerJinal PandyaAbinah Thevanayagam
Shannon EagleTzitziki LoezaKate PareAttilio Tonin
Tyler ElliottEddie MaOla PierossiNervana Wadie
Nicole FahnerKatie McGeeAdriana RaduloviciCatherine Wei
Becky FernandesTroy McMullinShahrokh ShekarrizMichael Wright
Kathryn HotkyeFatima MitterboeckAnjali SilvaRobert Young

Thursday, September 3, 2015

Primer bias in microbial diversity studies

The most intriguing result is that all these innovative, high-throughput molecular methods have their serious inherent biases. For example, amplicon-based methods depend strongly on taxonomic resolution of the barcode (DNA fragment used for identification), primer-template mismatches, the presence of introns and the overall length of the barcode; but conversely, PCR-free methods are affected strongest by the availability of taxonomic reference information, which differs enormously for fungal classes and phyla.

Motivated by criticism of a Science article on global fungal diversity, where the abundance of certain fungi were suspected of being underestimated, the authors went back to the lab to test if their initial approach may have involved a primer bias, i.e. distorted taxon distribution as a result of imperfect primer matches with some templates in their application of metabarcoding. 

What a great example of serious science. The authors took the criticism, went back to the drawing board, did experiments and published their findings in two journals (as response in Science, and the full study in MycoKeys) even though those confirmed doubts about some results in their earlier paper. There is no need to retract any paper but the colleagues re-checked some of their results and had the guts to write about it. Their new findings are immensely important for the community at large which makes this even more commendable. Some might wonder why I am so excited by this. Well, in times where the amount of retracted papers in big journals increases and the reasons for this are mostly rather embarrassing for the scientific community (e.g. falsification, non-reproducible, methodologically flawed), every example that shows how it is supposed to be done is more than welcome. Also, quite often responses and comments in scientific journals are more representative of personal conflicts between scientists than constructive dialogue meant to advance our knowledge.

And the results? 
The colleagues demonstrated substantial methodological biases in soil fungal diversity. High-throughput Illumina sequencing of DNA metabarcodes and the whole soil metagenome revealed strong methodological biases in taxonomic insights into soil fungal diversity. All methods had their inherent biases and shortcomings, but reached roughly similar ecological conclusions indicating the greatest role of floristic variables on soil fungal communities in the mountainous Papua New Guinea. 

This study demonstrates that PCR-free metagenomics and amplicon-based approaches perform in a comparable fashion in recovering major fungal classes in spite of certain statistical differences. Within the amplicon data set, barcode-primer pair combinations differed strongly in recovering relative abundance of fungal classes and OTU richness (see also Tedersoo et al. 2015b). Nonetheless, these were all in agreement about trends in OTU richness and disentangling the key drivers of community composition. We found no evidence for reduced statistical performance in barcodes with relatively conserved sequences, but the use of conserved barcodes seriously hampers biological relevance of the data due to the inability to approximate species level (or explicitly any taxonomic level) and to assign functional categories such as trophic status (except arbuscular mycorrhizal mutualism). Considering the taxonomic resolution and primer bias, we recommend targeting the ITS2 barcode when using the current HTS [High throughput] technologies that permit <700 bases of high-quality reads.

Wednesday, September 2, 2015

DNA Barcoding in exams

It is not news that DNA Barcoding is slowly finding its way into schools by a variety of programs and ideas. A few years ago it found its way into a widely used North American Biology Textbook (see image). Meanwhile it is usually treated as a generally accepted methodology and very often you'll find a paragraph or two in some high school textbooks.

It turns out it is also used in some official high school exams. I just learned that a question on DNA Barcoding appeared in the International General Certificate of Secondary Education (IGCSE) exam in 2014. The IGCSE is an academically more challenging, international curriculum which is offered to students to prepare them for International Baccalaureate and other levels recommended for higher tier students. Here we go - would you know the answer?

h/t John-James Wilson

Tuesday, September 1, 2015

Genetic diversity in threatened vertebrates

Threatened or endangered populations are identified and ranked by varying methods across states, countries and organizations, but criteria typically are based on demographics.

The International Union for Conservation of Nature (IUCN), for example, identifies species of conservation concern based on the number of mature adults in a population, range size and evidence of population decline. Animal species on IUCN's Red List, the most comprehensive record of threatened species worldwide, are ranked by estimates of how close to extinction they are. However, the criteria currently used to identify at risk species are not correlated with genetic diversity. This suggests that some threatened species could be overlooked because populations with low genetic diversity may not be able to adapt to challenges such as changing environmental conditions, shrinking habitats or new diseases, which could put them at risk of disappearing. 

A new study presents a novel approach for identifying vertebrate populations at risk of extinction by estimating the rate of genetic diversity loss, a measurement that could help researchers and conservationists better identify and rank species that are threatened or endangered.

Genetic diversity is a key component to the long-term survival of a population.The approach we developed identifies populations with limited genetic diversity that isn't going to be enough to allow the population to persist over time. We found that this method performs significantly better than current methods for identifying species in need of conservation efforts.

The colleagues conducted a review of vertebrate genetic data published since 1990 to investigate the relationship between genetic diversity and the at-risk status of animal species. The team used microsatellite datasets from 5,285 studies spanning 17,988 loci to estimate genetic diversity (heterozygosity and allelic richness) across wild populations of birds, fish, reptiles, amphibians and mammals. They found that threatened species had reduced genetic variation, likely due to inbreeding and the random loss of variation that occurs when population sizes are small.

Unless a population with poor genetic diversity has undergone a dramatic decrease in size, it could be overlooked with our current methodology. We should consider genetic diversity in conservation rankings so a species doesn't go extinct simply because it wasn't on our radar.

The team then examined IUCN's criteria for classifying threatened species to determine how effective the criteria were at identifying genetically poor species. If genetic diversity estimates correlated with the Red List criteria, then IUCN would be systematically selecting for populations or species that have declining diversity, the researchers reasoned. However, they found that IUCN's criteria were not closely linked to genetic diversity.

The criteria of many conservation organizations were formulated before the availability of genetic data we have today. But genetic methodology has advanced so rapidly that factoring in genetic diversity is now pretty straightforward. Therefore, we propose that IUCN incorporates an additional criterion that addresses effective population size and genetic diversity for the use in ranking conservation priorities.