What’s new

DNA barcode course at Lake Baikal

19/09/2018

lake-baikalLake Baikal. Photo: T. Ekrem CC-BY.

An increasing part of biodiversity research and nature management is about the mobilization of biodiversity data. This can be species occurrences, genetic diversity, ecological preferences, and other types of biological information. Accessing such information effectively is often not quite straight forward, but with a little bit of introduction and practice, it is amazing what can be achieved.

This was the rationale behind the ForBio course Data mobilization skills: training on mobilizing biodiversity data using GBIF and BOLD tools held in Naratey on the western shore of Lake Baikal September 14-20, 2018. Together with the Siberian Institute of Plant Physiology and Biochemistry Russian Academy of Sciences (SIPPB SB RAS), University of Bergen, and the Global Biodiversity Information Facility (GBIF) Secretariat, NorBOL participated in teaching data mobilization skills to Russian and Norwegian students. The course was funded by the Norwegian Centre for International Cooperation in Education (previously SIU, now DIKU), GBIF and the Research School in Biosystematics (ForBio).

Group_photo-baikalStudents and teachers of the course at Lake Baikal. Photo: Dimitry Schigel CC-BY-SA 4.0.

A total of 16 students attended the five-day course, enthusiastically participating in 20 different sessions of lectures and practical exercises. The barcoding part of the course included theory and practice for providers and users of DNA barcode data. There was extensive use of BOLD, and the students explored various parts of the workbench including basic structure, submission of data, and analytical tools. This was new to most students, but we were impressed by how well they worked together to find solutions and teach each other valuable tricks.

bold-practiceEnthusiastic participants working with BOLD Systems. Photo T. Ekrem CC-BY 4.0.

The course did not stop there. The students also got an introduction to molecular systematics and the MEGA software, and used this to further explore trends and relationships in the available DNA sequence data. How should one interpret phylogenetic trees? What is the real difference between maximum parsimony and neighbour joining trees? Why do we need substitution models?

To finish off the course, the students presented projects they had developed for the Baikal Biodiversity Challenge. In this task, they designed inventory projects for selected taxonomic groups in the Lake Baikal area, taking present knowledge, cryptic diversity and data mobilization into account. Great work and good results from all groups!

Thank you to the BOLD support team for facilitating the live interaction with BOLD-Systems, and to all the students for their fantastic efforts.

baikal-selfie-largeHappy barcoders with #mydnabarcode scarfs. Photo: Laura Russell CC-BY-SA 4.0.

Katrine Kongshavn & Torbjørn Ekrem

DNA barcoding of Norwegian water mites

29/11/2017

Living water mites can look like moving gems in benthic samples from freshwater habitats. What do we know about these fascinating creatures, and how easy is it to barcode them?

Sperchon glandulosusSperchon glandulosus, a common species in low and middle order streams. Photo Reinhard Gerecke.

True water mites are 0.2-5 mm large arachnids that are commonly found in all kinds of freshwater. Under undisturbed conditions, they are particularly frequent and species-rich in lakes, running waters and springs. They are generally recorded also from peat bogs and temporary ponds. Water mites constitute an important element in freshwater ecosystems and many species have specific habitat requirements. This make them suitable for biomonitoring, but extended use is hampered by challenging taxonomies and size. Thus, DNA barcoding would be an excellent tool to increase the use of water mites in freshwater assessments.

This is one of the reasons why we (Elisabeth Stur, Gaute Kjærstad and Torbjørn Ekrem) at the NTNU University Museum started building a reference library of Norwegian water mites. We managed to convince world expert Reinhard Gerecke to collaborate with us to have Norwegian and Greenland water mites identified and barcoded.

The diversity and distribution of Norwegian water mites are poorly known: current unrevised lists comprise about 150 species, mostly recorded from eastern Norway only. At the same time, several species have their type localities in Norway, being first described by the Norwegian priest and arachnologist Sig Thor (1856-1937). This makes knowledge of the Norwegian fauna taxonomically important in a wider perspective, as recently exemplified by Pešić et al. (2017) in their revision of the Hygrobates fluviatilis complex.

When we started our project, there were no records of water mites from Norway and Greenland in the Barcode of Life Data Systems (BOLD). Now there are sequences of 22 identified species from Norway and 3 species from Greenland. Although this only is a very small percentage of the expected fauna, it is a proof of concept for DNA barcoding in Norwegian water mites: DNA barcodes are well suited to identify species and can be used to detect cryptic diversity. One example for this is the species Lebertia porosa, first described by Sig Thor in 1900 and with the high number of 37 junior synonyms. This species has no less than 7 BINs in our dataset and is a good candidate for thorough taxonomic scrutiny.

Lebertia porosaThe water mite Lebertia porosa has seven BINs in Norway. Photo Reinhard Gerecke.

Moreover, we tested two different ways of DNA extraction from sampled tissues: Dissection of legs or non-destructive extraction from whole specimens. Both methods performed equally well with a success rate of 84%. Thus, there are multiple options to preserve vouchers for DNA barcodes.

Given the high diversity and importance of water mites in freshwater ecosystems, the knowledge of the Norwegian fauna would gain much from an inventory project on this group. It is also obvious that a proper representation of identified water mites in the barcode reference library is needed to fully appreciate future environmental barcoding in assessments and management of freshwater ecosystems.

Elisabeth Stur, NTNU University Museum

New midge species named after Paul Hebert

19/10/2017

In an article recently published in the journal Insect Systematics and Evolution, Xiaolong Lin describes eight species of non-biting midges new to science.

“It is particularly rewarding to find and describe new species from a well investigated area such as Norway” says Lin, “but also exciting to find new species from my home country China”.

Non-biting midges, or chironomids, are small insects, and a compound microscope must be used to see the subtle differences between closely related species. However, they are easily separated by DNA barcodes.

“Because several of the new species first were detected using DNA barcoding, it was a natural thing to name one of them after the father of DNA barcoding Paul Hebert”, Lin explains. “The fact that this species is found in Arctic Canada, an area where Hebert have worked intensively, was particularly nice”, he says.

Tanytarsus heberti, the small midge of 2,5 mm from Churchill and Wapusk National Park in Manitoba, can be separated from its closest relatives by its lighter body colour, small details in the male genitalia and a characteristic DNA barcode.

Co-authors and supervisors Elisabeth Stur and Torbjørn Ekrem at the NTNU University Museum elaborates:

“Xiaolong has done a very thorough and good investigation of this group of non-biting midges. Not only does he describe new species in his thesis, but he analyse their evolutionary relationship and geographical distribution. This is a great contribution to our knowledge of a species rich and important group of insects”.

Xiaolong LinDr. Xiaolong Lin post defence of his PhD-thesis at NTNU. Photo: Torbjørn Ekrem CC-BY.

Lin, X., Stur, E. og Ekrem, T. 2017. DNA barcodes and morphology support new species in Chironomidae (Diptera). Insect Systematics and Evolution XX:00-00.

Symposium Biodiversity and Humanity

19/05/2017

The NTNU University Museum and the Norwegian Biodiversity Information Centre has the pleasure of inviting you to the symposium Biodiversity and Humanity in Trondheim, a side-event of the Starmus-festival. Six international capacities, including Nancy Knowlton and Paul Hebert from the festival main program will reflect on biodiversity and how we as humans have influenced life and are being influenced by life on earth. Other speakers are Tom Gilbert, Maria Capa, Sujeevan Ratnasingham and Hans Stenøien. Please see Biodiversity and humanity program 2017 for details.

The symposium is free of charge and is held 22 June at 09:00 i Akrinn, Sverresgate 12. We invite all participants for lunch after the talks, so please register here: https://ntnu.wufoo.eu/forms/registration-for-biodiversity-and-humanity/.

At the time of the symposium, the NTNU University Museum hosts the world famous exhibition Body Worlds Vital. Tickets for the exhibition are sold separately.

We hope to see many of you at the symposium!

Best wishes,

Torbjørn

Paul Hebert to talk at the Starmus-festival

07/03/2017

What does Stephen Hawking, Buzz Aldrin, Paul Hebert, Oliver Stone and 10 Nobel Laureates have in common? They will all speak at the Starmus Festival: Life and the Universe in Trondheim, June 18-23, 2017!

STARMUS – Life and the Universe

Starmus is a grandiose festival. With it’s star-speckled list of speakers and artists, Starmus has as goal to bring an understanding and appreciation of science to the public at large. This is the fourth Starmus festival and as in previous years, astronauts, physicists, astrophysicists, biologists and musicians will be speaking about life, the universe and things that (dark) matter. The program is still under development, but it is already certain that the festival in Trondheim might become a ‘once in a lifetime experience’.

So, what will the ‘father of DNA barcoding’ Paul Hebert speak about in this setting? Could it be the Planetary Biodiversity Mission? The microbiologist Emmanuelle Charpentier, the molecular biologist Susumu Tonegawa, the astrobiologist Nathalie A. Cabrol, the marine biologist Nancy Knowlton and the neurobiologists May-Britt and Edvard Moser are other famous biologists in the program.

In addition, three moonwalkers will have a public conversation about the moon and beyond. That will also be interesting, guaranteed.

moon-and-beyond

DNAqua-Net: a COST-Action for developing new genetic tools for bioassessment of aquatic ecosystems in Europe

01/11/2016

dnaqua_net-logo

From the COST-Action CA152119 websiteThe protection, preservation and restoration of aquatic ecosystems and their functions is of global importance. For European states it became legally binding mainly through the EU-Water Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch thus obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawback such as being time consuming, limited in temporal and spatial resolution, and error-prone due to variation of individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforesaid problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel eco-genomic indices for routine application for biodiversity assessments of European water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians and other stakeholders, the group will develop a conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments.

The inaugural meeting of DNAqua-Net was held in the COST-building in Brussels on October 20, 2016. The COST-Action was formally accepted and chair and working group leaders were elected. So far 31 countries are associated with the action, med representatives in the Management Committee nominated by national COST-coordinators. The delegates from Norway are Trude Vrålstad (Norwegian Veterinary Institute) and Torbjørn Ekrem (NTNU University Museum). The first conference of DNAqua-Net will be held in Essen, Germany, March 6-8, 2017, with post conference meetings in the five working groups (leads in parentheses):

  • DNA Barcode References (Torbjørn Ekrem, Norge + Fédor Ciampor, Slovakia)
  • Biotic Indices & Metrics (Jan Pawlowski, Sveits + Maria Kahlert, Sverige)
  • Lab & Field Protocols (Kat Bruce, UK + Emre Keskin, Tyrkia)
  • Data Analysis & Storage (Kessy Abarenko, Estland + Diego Fontaneto, Italia)
  • Implementation Strategies & Legal Issues (Patricia Mergen, Belgia + Daniel Hering, Tyskland)

participants-dnaqua-net-meeting-brusselsParticipants at the inaugural meeting in the COST-Action DNAqua-Net.

Natural History Museum at the Oslo Science Fair

01/11/2016

The Natural History Museum in Oslo and NorBOL participated at the Oslo Science Fair September 23-24, 2016. At our stand we communicated challenges with biological, morphological and genetic species definitions. Fifteen hundered shots of juice were served with the task of identifying which three fruits the juice was composed of. To help them with the task, people received visual DNA barcodes of the fruits as well as a reference library of fruit barcodes. Many learned how DNA barcoding can be used to determine the content of food.

Gunnhild med juicenGunnhild Marthinsen serves unknown juice at the Oslo Science Fair. Photo Dag Inge Danielsen CC-BY.

juice-testingPhD-student Sonja Kistenich shows how DNA barcoding works. Photo Gunnhild Marthinsen CC-BY.

Gunnhild

NorBOL at Researchers’ Night 2016

01/11/2016

On Friday September 23 time had come for Researchers’ Night in the NTNU Science Building. Like previous years, the interest for participation was great and more than 1100 high school students trawled the stands, attended lectures and visited labs at NTNU. NorBOL was present with a stand on DNA barcoding and LifeScanner.

NorBOL at RNXiaolong and Aina welcome visitiors to NorBOL’s stand at Researchers’ Night 2016. Photo Torbjørn Ekrem CC-BY.

At our stand, students and teachers were challanged to do practical DNA barcoding: Three visualized DNA sequences from unknown prey had been retrieved from a boreal owl pellet and could be compared to known sequences in a reference library. The task was not necessarily simple and created good discussions among the participants. As prize and proof of particpation, the stydents received #mydnabarcode stickers.

Referansebibliotek RNTorbjørn explains how DNA barcoding works. Photo Xiaolong Lin CC-BY.

https://youtu.be/sAEwEpzP_ko

Active visitors at the NorBOL stand. Video Torbjørn Ekrem CC-BY.

Thanks to Aina, Erik and Xiaolong for excellent contributions to the NorBOL stand and Researcher’s Night!

Torbjørn

Mushroom Day at Tromsø University Museum

06/09/2016

Every year in the mushroom-season, the Tromsø Mushroom Society arrange mushroom check-points at the Tromsø University Museum where the general public can have their collected mushrooms identified. They also invite to guided tours and celebrate “Mushroom Day”. NorBOL attended all check-points so far this year and has received plenty of species for DNA barcoding.

Sopp fra soppens dagOne of the sampled mushrooms: Hygrocybe cf. pratensis. Photo Marie K. Føreid Merkel CC-BY.

“Mushroom Day” was held at Tromsø University Museum on September 4th and included an exhibition of freshly picked specimens as well as the regular check-point and a local guided tour. NorBOL attended the event and received about 20 new species for barcoding. Most of these came from the exhibition made by the Mushroom Society, but some were also donated by the visitors.Sopputstilling på soppens dagMushroom exhibition on Mushroom Day. Photo Marie K. Føreid Merkel CC-BY.

During collection of specimens for the exhibition, one new species to North Norway was found. This specimen will be barcoded. NorBOL staff used the opportunity to talk to visitors about DNA barcoding, the work that they do and how mushrooms are preserved and stored in the scientific collections at the museum. So far, NorBOL har received more than 120 species from the area of Tromsø, with great help from the Mushroom Society.

We hope that the last to check-point dates (11 and 18 September) will bring in even more specimens, and that we can continue our outreach on DNA-barcoding to the general public. Thanks to the Tromsø Mushroom Society for excellent collaboration!

Marie K. Føreid Merkel

Barcode of Life conference heading for Kruger National Park

04/08/2016

Imagine this: You wake up before the sun rises, find your guide and get set for today’s “morning drive” to watch elephants, lions and rhinoceros as the first rays of sun hit the bushland. You return to the camp and enjoy an excellent breakfast before the first plenary of the day on environmental barcoding of North American wetlands. This dream can come true before you realize: The seventh Barcode of Life conference will be held in Kruger National Park, South Africa, 20-24 November 2017.

Photo: T. Ekrem CC-BYElephants in South Africa. Photo Torbjørn Ekrem CC-NC-SA.

The international conferences on DNA barcoding have been held every second year since 2005 (in London) and have continuously increased in size and content. The participants come from all over the world and present their research, educational programs and public outreach initiatives. All aspects of DNA barcoding and metabarcoding are covered and the presentations can include anything from development of methods and taxonomy to citizen science, applied ecology and nature management. The last meeting in Guelph (2015) had 600 participants from 60 countries. Time will tell if the upcoming meeting can beat those numbers…

The scientific program for the meeting is under development, but several invited speakers have already accepted. The theme of the conference will be “Exploring mega-diverse biotas with DNA barcodes”. Registration will open December 1, 2016 and end November 1, 2017. The main lecture hall has room for 700 guests, so the meeting probably will not be fully booked the first week. Nevertheless, it might be a good idea to sign up early!

See you in Kruger!