New issue Barcoding Bulletin

Hot off the press - the fall issue of our Barcode Bulletin newsletter (just click on the image for download):

Enjoy reading!

Key pollinators in the Arctic

Dryas flowers. Credit: Mikko Tiusanen

Global change is causing drastic changes in the pollinator communities of the Arctic. While arctic flowers are visited by a wide range of insects, flies in family Muscidae have been proposed as a pollinator group of particular importance.

Researchers from Finland, Sweden, Denmark and Canada teamed up to record what insects visited flowers of the evergreen dwarf shrubs of the genus Dryas. They chose 15 sites in northeast Greenland, then returned to score the seed set of these flowers to determine if it actually has been pollinated. The results were clear: the more of the house fly -like relatives of the family Muscidae were present, the more flowers set seed. Among these flies, a single spcies best explained seed set, Spilogona sanctipauli.

To record the insects visiting a plant, the researchers invented self-trapping flowers. They cut sticky traps for greenhouses into the shape of natural looking flowers and hid those among the real ones. This saved them from the alternative which would have been to stare at the flowers for a long time to record flies that land on the flower. DNA barcoding was utilized to identify all their victims (some 8000 of them).

While exciting, the current findings also raise concerns. The very same flies which were found to be so important for Dryas species are now declining in this region. Part of this decline may be due to an increasing temporal mismatch between the occurrence of the flies and their flower resources. To test this hypothesis, the researchers recorded if insects visited flowers early versus late in the season, i.e., during peak flowering or later, when there are less flowers in bloom. They found that many insects visited after peak flowering. 

This quite worrying as with the warming of the arctic, flowering time will shift to earlier times, whereas insects seem to be able to adapt to that. Hence, we actually see the timing of avens sliding into the early summer when less flies are there to service the flowers. For the plant, this means less pollinators, and for the flies, this means less food. If this rift expands, then this may threaten arctic pollination.

eDNA to detect invasive crayfish

Globally, there are around 600 crayfish species, of which only about a half dozen have become problematic invaders in North America. These non-native crayfish prey on fish eggs and destroy aquatic plants, and can negatively affect fish through competition for food and changes to their habitat.

There are economic repercussions from invasions. One eradication of rusty crayfish in Wisconsin took years and was very costly.In that instance, success may have been due to a drought that substantially lowered the lake levels and stranded their habitat. Crayfish can walk over land so if you have them in an aquaculture pond there's nothing to prevent them from crossing over a little hill and then showing up in a national park. They're also prevalent in elementary and middle school science classrooms as live animals for behavioral studies. Teachers may not want to euthanize the crayfish at the end of the school year. Often believing that there is just one crayfish species everywhere, they have an end-of-semester release party and dump aquarium contents into a local pond or stream, or send crayfish home with students who may subsequently release them.

Researchers of the University of Illinois developed an eDNA based assay to detect the invasive rusty crayfish Orconectes rusticus in Lakes across Wisconsin and tested if the method is suitable to determine its relative abundance. They used COI DNA barcodes in combination with qPCR. 

We detected Orconectes rusticus eDNA in all lakes where this species was collected by trapping, down to low relative abundances, as well as in two lakes where trap catch was zero. Detection probability of Orconectes rusticus eDNA was well predicted by relative abundance of this species and lake water clarity. However, there was poor correspondence between eDNA copy number and Orconectes rusticus relative abundance estimated by trap catches.

As with many studies using eDNA to identify and track organisms in various aquatic ecosystems, the simple presence/absence detection works quite well and only needs calibration as the method is usually very sensitive. However, this study shows once more that a quantitative eDNA technique has yet to be established.

Marine extinctions: the big ones go first*

There is strong evidence that populations of large marine animals have declined considerably in recent times. This decline is generally attributed to increasing fishing pressure, the effects of which in groups like sharks and rays are accentuated by the generally slow growth, late maturity and low reproductive output. Other major threats to oceanic life include habitat alteration, damage and loss from coastal developments, pollution, and the impacts of fisheries on the seabed and food species.For instance populations of Oceanic whitetip shark shrank by 93%, hammer heads by 89% and great whites by 80%. Some tuna species are sold at record values simply because they became so rare. The list continues and it is a new phenomenon that especially larger species are disappearing.

A new study by US researchers found that extinction threat in the modern oceans is strongly associated with large body size, whereas past extinction events were either nonselective or preferentially removed smaller-bodied taxa. Pelagic animals were victimized more than benthic animals during previous mass extinctions but are not preferentially threatened in the modern ocean. The differential importance of large-bodied animals to ecosystem function portends greater future ecological disruption than that caused by similar levels of taxonomic loss in past mass extinction events.

Many of these larger species are top predators that help to control the population sizes of smaller species. Removal of large-bodied predators can trigger trophic cascades affecting many other species. One of many examples is the explosive population growth of  the crown-of-thorns sea star (Acanthaster planci). Colleagues attribute this to the loss of giant triton (Charonia tritonis), one of the few species that can actually feed on the star fish. The snail shell is unfortunately massively harvested as decorative object.

The loss of large taxa may have caused more ecological disruption than the loss of comparable numbers of smaller taxa; indeed, loss of large animals may explain in part the multimillion-year delays in ecosystem recovery following these catastrophes. The preferential removal of the largest animals from the modern oceans, unprecedented in the history of animal life, may disrupt ecosystems for millions of years even at levels of taxonomic loss far below those of previous mass extinctions. And, unfortunately, the lack of correlation between the proportion of species assessed within higher taxa (phyla, classes, and orders) and the proportion considered threatened for marine animals suggests that the pessimistic projection of future genus losses may more closely approximate the true threat level than the optimistic projection. Without a dramatic shift in the business-as-usual course for marine management, our analysis suggests that the oceans will endure a mass extinction of sufficient intensity and ecological selectivity to rank among the major extinctions of the Phanerozoic (541 Ma to present).

*Title "stolen" from a Twitter feed by Jon Lefcheck

Diversity along an urbanization gradient

Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. 

University of Washington and Northwest Fisheries Science Center research has applied eDNA technology to broadly measure the effects of human activity on the environment. In a new paper just published in PeerJ, researchers describe how they used DNA in the waters of Puget Sound, Washington state, to characterize the amount of animal life along highly urbanized shorelines, such as Piper's Creek in Seattle, and in more remote areas with fewer humans, like Vashon Island. This is believed to be the first study that uses genetic markers to understand the impact urbanization has on the environment, specifically, whether animal diversity flourishes or suffers.

The study detected more than 1,600 unique genetic signatures - many representing different species - across Puget Sound, including porpoises, salmon, starfish, barnacles, eagles, and even humans. The colleagues also found that urban Puget Sound shorelines support a denser array of animals than in remote areas. In particular, clams and other mud-dwellers congregate more densely along urban beaches which the researchers consider a surprising find:

Clams and other things that live in mud seem to like living near cities, which is really interesting. It suggests that maybe humans are subsidizing mudflats, or it may just as well be the converse - maybe humans tend to live in really protected areas that are the same environment clams happen to like.

While urban beaches in Puget Sound had more abundant fauna, these areas were also more homogenous in the kinds of species that lived there, the researchers found, suggesting a trade-off between different kinds of diversity between more- and less-urban areas.

We can go out, take a sample of water, and the DNA from thousands of species appears. This way, we don't have to decide if we are going to count snails or orcas when we look at environmental impacts. Instead, we can just look at what's there. 

From the inbox: The Roddenberry Prize

Maybe time to really build the Tricoder (with DNA barcoding integrated).

Roddenberry Foundation Celebrates StarTrek50 With An Innovation Competition

To commemorate the 50th anniversary of the television premiere of Star Trek, the Roddenberry Foundation announced a million dollar prize competition to encourage innovation that will build a 'boldly better' future. The inaugural Roddenberry Prize consists of one $400,000 grand prize and four $150,000 innovation awards, disbursed in lump sums to five recipients, complementing several new foundation initiatives. 

Each year the Roddenberry Prize (like the foundation, named for the creator of Star Trek) will recognize five ideas that will help bring about the vision of the future presented in Star Trek.  The prize fits in with the other work of the foundation, which is focused on supporting people and institutions looking to improve the human condition.

The goals are broad, and science and technology are just one of the broad categories wherein we can build the better future we've been watching for half a century.  The judging criteria are perhaps the best way of trying to envision the entries contest organizers want.  They are looking for solutions notably distinct from other efforts in the same area and capable of transforming the intended audience.  All the same, entrants will have to demonstrate their capability of implementing their idea through a combination of their skills, experience and plans.

The competition window is short, running from September 8 to November 16.  The winning entries will be recognized in January (trying to build synergy with the new Star Trek series expected to premiere at the same time).  The prize money is intended to support the expansion of the winning ideas to a larger scale. 

The application deadline is November 16, 2016.

One more time...

Next week our famous School Malaise Trap program will start to another hopefully successful fall run. The traps have been shipped and arrived at most of the schools. Some more remote ones will get them in the next few days. 

Once again we have selected 60 Schools and some reference sites. As usually we had many many more schools that wanted to participate but with limited resources we can only accommodate for this number. Unfortunately, it also looks like we won't have any funds to continue the program in the future. This is of course very frustrating especially given the continuing huge interest of schools across the country and elsewhere. In the last few years we brought this program in some 400 classrooms with thousands of students. It became well-known as an exemplary way of inquiry based, hands-on learning in STEM. Yet, this didn't help much. We approached quite a few foundations and applied for funding but none seems to be interested to pick up the rather large bill. A run costs something between $800 and $1000 per school, which is way over the spending limit of most schools. The fact that we had the funds to subsidize all past runs allowed them to be part of the project. It is a sad reality that there isn't much money for school education to begin with (or maybe it is just spend elsewhere). Most teachers in Canada have to work on a budget that is shockingly small. I wonder how we ever going to provide the proper STEM education needed to prepare students for the challenges of the future?

At this point our only hope for a comeback lies in the advancement of technology. New HTS technology and metabarcoding might come to our rescue. At some point they will allow us to reduce the costs for the analysis of a single trap catch to a point that it becomes affordable for schools even on a shoestring budget. Unfortunately, we are not there yet. 

To end on a light note - I am looking forward to this last run as I did to all the ones over the past 3 years. We already received blog posts from schools all over the place and one can sense how the excitement builds in the classrooms. I am glad and proud that we were able to bring this to many students in our Country for a few years.

Forecasting biodiversity under climate change

As global climate change accelerates, one of the most urgent tasks for the coming decades is to develop accurate predictions about biological responses to guide the effective protection of biodiversity. Predictive models in biology provide a means for scientists to project changes to species and ecosystems in response to disturbances such as climate change.

However, current models are not performing very well and don't provide accurate predictions. One reason is that most of them do not include biological mechanisms such as demography, dispersal, evolution, and species interactions although these have been shown to be connected to climate change responses. Most models are descriptive, based on statistical correlations and observations, and fail to capture the underlying processes that produce observed changes. For example, a descriptive model might show that lynx in the northern U.S. are declining while bobcat populations in the same region are on the rise. Understanding what is driving this change requires a different sort of model, one that incorporates biological mechanisms. A mechanistic model that accounts for how warming temperatures affect snow depth, for instance, could provide insights into why bobcats - better adapted to habitats with less snow - are gaining a competitive edge over lynx.

Another challenge is that as models have grown in sophistication, they have far outpaced data collection. Put another way, a model is like a state-of-the-art kitchen, but the cupboards are bare.

We can now build videogame-like environments with computers where we can create multiple versions of Earth and ask what the implications under different scenarios are. But our ability to learn from these tools is constrained by the kinds of data we have.

An international group of researchers identified six biological mechanisms that influence wildlife's responses to climate change: 

• physiology
• demography and life history
• evolutionary potential and adaptation
• interactions between specie
• movement over land or water
• responses to changes in the environment. 

They ranked the information needed to account for these mechanisms in models and suggested proxies for data that are missing or hard to collect. A globally coordinated effort to fill data gaps could greatly advance improvements in models and informed conservation approaches and local and regional conservation groups need not wait for a global body to coalesce to start using a mechanistic approach in their own region,.

If the ideas put forth in this paper start to be adopted and integrated into climate change work in a grass roots way, that could make a big difference in a region and could scale up over time.Working with citizen scientists offers an opportunity to get huge amounts of data, and it's foolish not to take advantage of it, The data might not be as rigorous and needs to be treated differently, but it's one more source of valuable information.

Another conference volume: Barcodes to Biomes

Not too long ago, I posted about a special barcoding conference issue the Philosophical Transactions of the Royal Society. The issue comprised of contributions derived from presentations at the 6th International Barcode of Life conference. As always there were so many good contributions that a single species issue doesn't do justice to the breadth and quality of talks and posters.

Well, I have good news - there is more. The Canadian journal Genome had agreed to publish a two-volume special issue as well. It was assembled by my colleague Sarah Adamowicz. I was one of the guest associate editors. The first volume was published today. And once more, all articles are Open Access. Enjoy reading:

From Barcodes to Biomes: Special Issues from the 6th International Barcode of Life Conference

Sarah J. Adamowicz, Frédéric J.J. Chain, Elizabeth L. Clare, Kristy Deiner, Vlad Dincă, Manuel Elías-Gutiérrez, Axel Hausmann, Ian D. Hogg, Mari Kekkonen, Darío A. Lijtmaer, Amanda Naaum, Dirk Steinke, Martha Valdez-Moreno, Michelle Van der Bank, John-James Wilson, Jianping Xu

The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

Tomas Roslin, Sanna Majaneva

Pollen DNA barcoding: current applications and future prospects

Karen L. Bell, Natasha de Vere, Alexander Keller, Rodney T. Richardson, Annemarie Gous, Kevin S. Burgess, Berry J. Brosi

DNA barcoding the Lepidoptera inventory of a large complex tropical conserved wildland, Area de Conservacion Guanacaste, northwestern Costa Rica

Daniel H. Janzen, Winnie Hallwachs

How to tackle the molecular species inventory for an industrialized nation—lessons from the first phase of the German Barcode of Life initiative GBOL (2012–2015)

M.F. Geiger, J.J. Astrin, T. Borsch, U. Burkhardt, P. Grobe, R. Hand, A. Hausmann, K. Hohberg, L. Krogmann, M. Lutz, C. Monje, B. Misof, J. Morinière, K. Müller, S. Pietsch, D. Quandt, B. Rulik, M. Scholler, W. Traunspurger, G. Haszprunar, W. Wägele

Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae)

Axel Hausmann, Scott E. Miller, Jeremy D. Holloway, Jeremy R. deWaard, David Pollock, Sean W.J. Prosser, Paul D.N. Hebert

Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation

Kristiina Mark, Carolina Cornejo, Christine Keller, Daniela Flück, Christoph Scheidegger

A quantitative protocol for DNA metabarcoding of springtails (Collembola)

Seikoh Saitoh, Hiroaki Aoyama, Saori Fujii, Haruki Sunagawa, Hideki Nagahama, Masako Akutsu, Naoya Shinzato, Nobuhiro Kaneko, Taizo Nakamori

Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea

Mamoon M.D. Al-Rshaidat, Allison Snider, Sydney Rosebraugh, Amanda M. Devine, Thomas D. Devine, Laetitia Plaisance, Nancy Knowlton, Matthieu Leray

DNA barcoding in the media: does coverage of cool science reflect its social context?

Janis Geary, Emma Camicioli, Tania Bubela

Can butterflies cope with city life? Butterfly diversity in a young megacity in southern China

Kong-Wah Sing, Hui Dong, Wen-Zhi Wang, John-James Wilson

Genetic diversity among populations of Antarctic springtails (Collembola) within the Mackay Glacier ecotone

Clare R. Beet, Ian D. Hogg, Gemma E. Collins, Don A. Cowan, Diana H. Wall, Byron J. Adams

Exposing the illegal trade in cycad species (Cycadophyta: Encephalartos) at two traditional medicine markets in South Africa using DNA barcoding

J. Williamson, O. Maurin, S.N.S. Shiba, H. van der Bank, M. Pfab, M. Pilusa, R.M. Kabongo, M. van der Bank

Food from Thought

The official federal announcement was made on Tuesday but today we had our own celebration on campus or more specifically at our institute. The University of Guelph is one of 13 happy recipients of funding from the Canada First Research Excellence Fund. The project that spans across several schools and departments on campus was awarded $76.6M over seven years for an ambitious project:

We share this planet with millions of species. A few feed us directly, while others are central to our planetary ecosystem. Population growth places us in conflict with the natural world, threatening major declines in global biodiversity. The grand challenge is to develop systems that are capable of meeting the rising human demand for food while being resilient to climate change, and able to sustain healthy ecosystems, economies, and populations.

Food from Thought will allow the University of Guelph to become the global leader in this field. It will do so by integrating existing strengths—such as the Biodiversity Institute of Ontario, and Canada’s largest network of agriculture and food research facilities—to support a unified scientific vision:

• to transform our understanding of the ecosystems we depend on for food, at scales that range from planetary to microcosmic; and
• to increase the capacity, sustainability and safety of food production systems, without undermining environmental health, ecosystem services, or livestock health and welfare.

The theme that ties these objectives together is the effort to move the study of each scale of ecosystem into the world of big data, by employing sensors that gather information in unprecedented volumes, and by developing the capacity to analyze, preserve and curate data.

Personally I am quite pleased about this outcome as I've invested a substantial amount of time and energy into helping to write the proposal. It is always nice to see when all that actually pays off and in this case for a project with so much potential impact and collaborative spirit. 

Some of you might want to know what that means for us or for DNA barcoding in general. Well, this substantial injection of cash will e.g. make sure that BOLD will stay with us for a long time and grow into what its inventor, Sujeevan Ratnasingham, hinted at during his talk at the conference last year. It also means job security for a number of people at the institute and it will allow us to participate at an exciting and meaningful project, showing once more the benefits of the barcoding technology. 

In short: We are still here and we are here to stay!