Tag Archives: barcoding

Bryozoan barcoding

Haeckel Bryozoa.jpg
By Ernst Haeckel – Kunstformen der Natur (1904), plate 23: Bryozoa (see here, here and here), Public Domain, Link You can also find the whole, gorgeous book by Haeckel here, courtesy of the Biodiversity Heritage Library

I have spent the past week and a half getting acquainted with a rather odd – yet beautiful – group of animals, the Bryozoa, moss animals. These colony-forming, mostly marine, animals are small as individuals, but the colonies can grow quite large. Globally there are around 5000 extant species recorded, with a further 15 000 species in the fossil record. We have colleagues in Oslo who work on both the fossil and the current fauna to better understand micro- and macroevolution, you can read more about that here (og her, på norsk).

Sampling site of barcoded Bryozoans in the BOLD database

Sampling site of barcoded Bryozoans in the BOLD database

This is the first attempt at barcoding bryozoans through NorBOL, and it shows (map above); hopefully we will get more dots on the map for our region soon!

This may not be an easy group to get genetic barcodes from, though – I’ve been in communication with several of the (wonderfully helpful!) experts in the field, and the consensus seems to be that getting a barcode (from the region defined as THE barcode, the 5’ end of COI) will be difficult, and that we may anticipate “..a colourful array of contaminants, as well as nuclear mitochondrial pseudogenes”. Yay. Well, we won’t know until we try!

Together with colleagues from the Natural History Collections in Gothenburg we have assembled a plate of tissue samples from Swedish and Norwegian bryozoan that I will send to the CCDB facilities for sequencing next week. We have an impressive 58 different species (1-3 specimens of each) included on the plate, as well as a few specimens that are (not yet) identified to species.

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Bicellariella ciliata for barcoding

Bicellariella ciliata for barcoding

The colonies can be branching, encrusting, lacelike, lumpy…and at times pretty close to invisible! I’ve had to spend some time looking for good illustrations to know what to sample from… there are often multiple species in a jar, as well as other animals – hopefully I managed.

The specimens on the plate

The specimens on the plate

We’re treating this as a trial plate: is it possible to barcode museum material of bryozoans through the general pipeline, or will we need to get creative?

I’ll make a new post once the verdict is in – let’s hope for surprisingly high success rates!


Some further reading:

Lee et al 2011: DNA Barcode Examination of Bryozoa (Class: Gymnolaemata) in Korean SeawaterKorean J. Syst. Zool. Vol. 27, No. 2: 159-163, July 2011 ISSN 2233-7687
DOI 10.5635/KJSZ.2011.27.2.159

Wikipedia has a nice post on Bryozoa

 

When amphipodologists meet.

It generally happens every two years. The event may be seen as a natural phenomenon – or maybe rather  a cultural phenomenon. I am sure it looks strange if observed from outside the community. A lot of people of all ages and affiliations meet up in places most of us usually did not even know existed, and we have the best week of our work-year.

Happy friends meeting in Trapani. (all photos: AH Tandberg)

Happy friends meeting in Trapani. (all photos: AH Tandberg)

The bi-annual International Colloquium on Amphipoda (ICA) is without doubt the scientific meeting I look most forward to.  Every time. The fun, the science, the amphipods, the friendships, the coffee, the familiar banter, the late nights and early mornings, the discussions – all in an atmosphere of friendship.

The Polish Amphipod-t-shirt edition 2017. (photo: AH Tandberg)

The Polish Amphipod-t-shirt edition 2017. (photo: AH Tandberg)

The first day of any ICA could be mistaken for a family-gathering – or the opening credits of any film about best friends. The room resounds of “oh – finally – there you are!”, “how are the kids/grandkids?”, “I missed you this last hour! Thought maybe you got lost since you weren’t here immediately” and not least “Come, let me give you that hug I promised!” Ten minutes later everybody will be organised by the large Polish group for some gathering or fun – and the rest of us are trying to find out how we can get one of the cool group-t-shirts the Łodz-group have concocted this year. Or maybe we should rather go for one of the other cool t-shirts picturing amphipods?

We do talk amphipods, of course. The incredible variety of the group (of animals – as well as people) opens up for a wide spectre of research-questions and approaches, and meetings allow time to learn from each other, get inspired, start new collaborations and share samples and ideas.

Most important: the science of amphipods. Loads of interesting talks and posters! (all photos: AH Tandberg)

Most important: the science of amphipods. Loads of interesting talks and posters! (all photos: AH Tandberg)

 

Those getting to the poster-session fast enough win the crochet amphipods... (photo: AH Tandberg)

Those getting to the poster-session fast enough win the crochet amphipods… (photo: AH Tandberg)

This years ICA was held in Trapani, Sicily – where prof Sabrina LoBrutto on a short one year notice had organised the meeting. The three days we met were packed with more than 60 talks, more than 60 posters and loads and loads of happy amphidologists. With the University situated right across the road from the beach, and a lunch hour long enough for both a coffee and a swim/sample search the friendly atmosphere stretched to drying towels on the railings of the university-hall and sea-salted hairstyles for many after lunch.

Keeping the atmosphere friendly: Beach, coffee and icecreams (all photos: AH Tandberg)

Keeping the atmosphere friendly: Beach, coffee and icecreams (all photos: AH Tandberg)

 

The scientifically helpful Japanese amphipod t-shirt. (now the rest of you should notice the morphological differences between the families). (photo: AH Tandberg)

The scientifically helpful Japanese amphipod t-shirt. (now the rest of you should notice the morphological differences between the families). (photo: AH Tandberg)

We always try to publish the Amphipod Newsletter to coincide with the ICA. You can download the newsletter both from the World Amphipoda Database and the Biodiversity Heritage Library (both places also have back-issues available for downloads). One of the features of the newsletter is a bibliography of amphipod-related literature, and a list of new taxa. Since last AN we have 79 new species, 14 new genera and 12 new families! Every AN includes an interview with one of the amphipodologists – this year you can get to know Wolfgang Zeidler and his Hyperiidea better.

The next ICA? In two years we meet in Dijon, France! I am already excited – and maybe there will be mustard-coloured t-shirts in honour of the location (or burgundy-coloured t-shirts)?  What I know already, is that it is going to be like meeting family.

Anne Helene

Aliens amongst us?

It certainly does not take a great leap of imagination to get from these Isopoda collected by the MAREANO programme to various science fiction monsters!

isopoda_images_resized

click to embiggen!

I just completed photographing and tissue sampling 95 specimens that will be submitted for barcoding through NorBOL  – we’ll send them to the CCDB-lab in Canada for sequencing, and upload the metadata and sequences in the BOLD database – fingers crossed for successful sequencing!

On the hunt for seaweeds!

The red, the green, and the brown

The red, the brown, and the green

This week the invertebrates are forced to take second place (!) as I have joined the master students participating on the course BIO309A – marine floristics out at our field station.

Lab work

Lab work

The course is the sister course to Marine faunistics that I joined in on last fall. The focus of this week is the macroalgae; the seaweeds that most people are (passingly) familiar with. (The micro algae have been covered in lectures and lab work back at BIO earlier.)

We are doing a mix of field work and lab work. Every day we go out and sample, and bring the catch back to the lab to identify it. 1-2 specimens of each species that is identified is destined to become barcode vouchers for NorBOL, and go through the by now fairly familiar route of photo-tissue sampling-preservation for inclusion in the museum collection as a voucher. Seaweeds fixate badly in ethanol, so instead we are pressing them and making herbarium specimens. So far we have about 50 vouchers (from almost as many different species), and the number is sure to climb as we continue working our way through the fresh stuff we just collected.

Collecting just outside the station

Collecting just outside the station

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Kjersti is explaining about the current habitat

Ah, such a hard day to be at sea!

Ah, such a hard day to be at sea!

Vivid!

Vivid!

Being ferried across to the island where we'll examine the tide pools

Being ferried across to the island where we’ll examine the tide pools

Nice location!

Nice location!

"that one!"

“that one!”

Kjersti is explaining the habitat

Hunting

Wave exposed!

Wave exposed!

I do "happen" to find some animals *on the lagae as well - here's a beautiful nudibranch, a Doto cf. maculata

I do “happen” to find some animals *on the algae as well – here’s a beautiful nudibranch, a Doto cf. maculata

Undercover amphipod

Undercover amphipod

Hydrozoans and two Aplysia punctata hanging out on a piece of Ascophyllum nodosum

Hydrozoans and two Aplysia punctata hanging out on a piece of Ascophyllum nodosum

Guest researchers: Mario

We started early with visitors for 2016; Mario arrived already on the 4th of January!

Mario, on his temporary spot in the lab, studying spaghetti worms.

Mario, on his temporary spot in the lab, studying spaghetti worms.

 

Mario’s home institution is the University of Antioquia, in Medellin, Colombia, and the contrast to snow covered (and/or rain swept) Bergen has been great; this was his first time having snow beneath his shoes.

 

 

 

Arne

Arne

Another of our polychaete collaborators, Arne Nygren from Sjöfartsmuseet Akvariet in Gothenburg (Artsprosjekt can be found here (NO)) seized the chance to visit as well, and together with the resident polychaetologists (Jon, Tom and Nataliya) it meant that we suddenly had an impromptu polychaete workshop on our hands 🙂

Being able to meet in person makes the work flow smoother all around, as work was delegated and plans concretized. 2016 is likely to be a year with much focus on the Polychaeta, as it is both the final year of the PolyNor project (ends in spring), and the year of the 12th International Polychaete Conference, which will be held in Cardiff, Wales.

 

During Mario’s month-long stay he was examining the collection of terebellids from West Africa and the museum’s collection of the bristle worm genus Pista, much of which will later be barcoded through NorBOL (for the Norwegian material) and MIWA (for our West African samples).

Pista cristata identified by Dr. T. Holthe, one of the most important experts on spaghetti worms, from University of Bergen. RCP. Photo: MHL

Pista cristata identified by Dr. T. Holthe, one of the most important experts on spaghetti worms, from University of Bergen. RCP. Photo: MHL

In his own words:

Eupolymnia nebulosa after one collecting trip to Lysefjord close to Bergen. Photo: MHL

Eupolymnia nebulosa after a collecting trip to Lysefjorden close to Bergen. Photo: MHL

I usually work on the morphology of just one of the several families of polychaetes, the Terebellidae, or spaghetti worms. This visit has been very important since we have been able to separate four Pista species from the North Sea, using both morphological and molecular tools. “The combination of these two different methods has been superb”.

Jon, Arne and I began this study during August 2014, but this undertaking seems like it will never end because we keep adding more material. The recent findings have been the significance of some characters that did not have taxonomical importance in the past. Now, they are the clues for splitting very close species.

But this is not enough; it was possible to identify 43 species of terebellids belonging to 16 different genera, from material collected along the West African coasts.

This is a high polychaete diversity in only one family. For example, we found three Lysilla species, in a region with only one recorded species. New species? Highly possible. One can only wonder what the diversity of the remaining families is?

Verticilate chaetae (bristles) from one of the polycirrinae species photographed through a microscope. Photo: MHL

Verticilate chaetae (bristles) from one of the polycirrinae species photographed through a microscope. Photo: MHL

Methyl-green staining pattern of one of Pista species. Photo: MHL

Methyl-green staining pattern of one of Pista species. Photo: MHL

 

 

 

 

 

 

 

 

 

All this was accompanied with a perfect view through the window, seeing it snow some days, or watching the Sun on the mountains in front; some times with white top mountains, some times with deep blue sky. A landscape like that never could be my company in my tropical city.

Snowy view from the lab window Photo: MHL

Snowy view from the lab window Photo: MHL

Thank you for visiting, it was very nice having you here – we wish you the best of luck with your next adventure in Antarctica!

Berthella sideralis, a rarity finally documented alive and barcoded!

The Pleurobranchidae sea slug species Berthella sideralis was described by the Swedish malacologist Sven Ludvig Lovén in 1846 based on specimens collect at Bohuslän, in southern Sweden not far from the city of Gothenburg. This species has hardly been mentioned in the literature after its original description, and no images of life species are to our best knowledge available in books, research papers or even web platforms – until now!

A synthesis of the morphological features of B. sideralis can be found in Cervera et al. (2010) who studied in detail two specimens collected during 1930’s in Trondheimfjord as part of a phylogenetic study of the genus Berthella.

Recently, in late November 2015 during a Museum scientific cruise – there is a blog post about this day of field work here – we collected one specimen in Hjeltefjorden (around Bergen) at 220 meters depth using an RP-sledge. This specimen is here documented and was recently genetically barcoded as part of our effort to barcode the Norwegian marine fauna through the NorBOL project.

A live specimen of Berthella sideralis. Ths scale bar i 5 mm. Photo: K. Kongshavn

A live specimen of Berthella sideralis. The scale bar i 5 mm. Photo: K. Kongshavn

Berthella sideralis is only known from Sweden and Norway. In Norway it has been reported between Bergen and Finnmark.

Reference: Cervera, J L., Gosliner, T. M., García-Gómez, J. C., & Ortea, J. A. 2010. A new species of Berthella Blainville, 1824 (Opisthobranchia, Notaspidea) from the Canary Island (Eastern Atlantic Ocean), with a re-examination of the phylogenetic relationships of the Notaspidea. Journal of Molluscan Studies, 66: 301–311.

-Manuel & Katrine

Door #9: Delving into the DNA

From the pre-PCR lab

From the pre-PCR lab

The four PCR-machines lined up

The four PCR-machines lined up

We are very fortunate in that we have a modern DNA lab available «just down the street» from us, as the University Museum is part of the shared Biodiversity laboratories (BDL) structure.

The BDL is a formalized cooperation between three research groups at Dept. of Biology (Marine biodiversity, Geomicrobiology and the EECRG), and two of the research groups at the University Museum. One of the senior engineers if this lab is a Museum employee, and from time to time we are also able to hire in other collaborators for specific projects.

 

 

 

Pipetting

Pipetting samples onto one of the plates that we fill with DNA-extracts

 

For the past couple of months we’ve had a technician – Morten – working on resolving some of the challenges that we run into when we work on COI barcoding of marine invertebrates.

Unlike many of the other groups that this method works exceedingly well for (like the Diptera), we are experiencing difficulties in obtaining DNA barcodes from a significant proportion of our samples.

IMGP0775-001We are currently focussing particularly on the Polychaeta (bristle worms), as this is the group we have submitted the majority of samples from in both our major barcoding projects: MIWA (Marine Invertebrates of Western Africa) and NorBOL (Norwegian Barcode of Life).

 

Morten has been working on obtaining DNA from the more problematic species, by troubleshooting and tinkering on various aspects of the ways we extract and amplify genes.

Basically there are more or less standardized ways of obtaining DNA, and these methods normally works well. Unfortunately (for various reasons) this is not always the case, and this is where we have to alter the protocols to see if we can find a way to retrieve the sample DNA from the specimens.

So far it looks quite promising; we’ve been able to fill in some of the most important “blanks” in our datasets – and we’re not done yet!

– Morten & Katrine