Category Archives: Student Projects

PhD thesis defence

On June 7th Nina Therese Mikkelsen presented her thesis ” Phylogeny and systematics of Caudofoveata (Mollusca, Aplacophora)” for a public audience.  She was questioned by the opponents dr Mikael Thollesson, University of Uppsala, and dr Suzanne Williams, The Natural History Museum of London, and did an excellent performance explaining the results of her studies.

Guest researcher: Marla

Marla, who has been visiting several times to work on our amphipod collections, sent us this “travelogue” from her longest stay. In her own words:

I am a third year PhD student, and my project is shared between the University of Southampton at the National Oceanography centre and the Natural History Museum in London. I am supervised by Dr Tammy Horton (NOC), Dr Andrew Gates (NOC), Dr Phil Fenberg (UoS), Dr Miranda Lowe (NHM), and Dr Andrea Waschenbach (NHM).

I spent 8 glorious weeks in Bergen working with the invertebrate collections at the Department of Natural History of the University Museum of Bergen (UiB) together with the wonderful Anne Helene Tandberg and Endre Willassen. Also a massive thank you to Katrine Kongshavn, Morten Stokkan, Jon Kongsrud, Luis Felipe Martell Hernández, Aino Hosia, Tom Alvestad, Nataliya Budaeva, Manuel Malaquias, Louise Lindbloom, and Kenneth Meland for your help in the lab and support with my project and lunchtime conversations!

I arrived to Bergen mid- September just in time for the 2017 UCI Road World Championships! As a huge fan (and very amateur road cyclist) this was such a bonus to have the chance to see it. The race took over the town, and one late afternoon Anne Helene and I climbed half-way up Mount Fløyen to watch the men’s Time Trial. The sun was out, the streets were packed, atmosphere was electric and we had prime seats–I couldn’t wait to see Chris Frome (GB) and Tom Dumoulin (NL) cycling in action.  It was a fantastic afternoon!

Anne Helene and I enjoying the afternoon UCI race from our prime viewing spot

The classic road graffiti to show support to the cyclists. Here Tom Dumoulin is forever immortalized on Mount Fløyen.

Tom Dumoulin won first place in the men’s Time Trial, Chris Froome took third.

Back in the lab…

I was working with amphipods from the family Phoxocephalidae from the Western African Waters, focussing particularly on the amphipods from the sub-family Harpiniinae [crustacea; Amphipoda; Phoxocephalidae; Harpiniinae]. Phoxocephalid amphipods are highly speciose and abundant in deep sea sediments globally. Species identity is critical to understanding mechanisms driving observed biodiversity patterns and to asses community change. The aim of the project while in Bergen was to use both DNA barcoding and traditional morphological taxonomic approaches in order to create a robust library of Phoxocephalidae species from the poorly known West African waters. Large scale projects such as Marine Invertebrates of West Africa (MIWA) provide the perfect opportunity for collaborative work! More about the MIWA-project can be found here.

The MIWA project submitted over 2700 tissue samples from over 600 morphospecies for DNA barcode sequencing, including Crustaceans, Echinoderms, Molluscs and Polychaetes. Out of these, 45 samples were from the family Phoxocephalidae, the target taxa. Working with Dr Anne Helene Tandberg and Prof Endre Willassen, the sequenced MIWA Phoxcephalid voucher specimens were dissected and mounted as permanent microscope slides to morphologically score them. Later, the phylogenetic analysis based on all molecular and morphological characters will be compared. Each appendage was photographed on the modular (Leica CTR6000) microscope and the images were stacked, resulting in incredible photos!

Harpinia abyssi P7. Photo: M. Spencer

As a result of some of this work, we think that we have identified 4 new species to the genus of Basuto. The genus was previously monotypic, with the type-locality in South Africa. Now we are awaiting the holotypes and paratypes to arrive so that we can compare. Together with Anne Helene, Endre Willassen and Tammy Horton, I am currently writing my first publication, formally describing these specimens as new species. Stay tuned for further updates!

Basuto specimen pereopod 5. Photo: M. Spencer

Basuto specimen Mandible, Photo: M. Spencer

At work in the DNA lab

Working with Anne Helene within the molecular biology labs at the University of Bergen, I had the chance to develop taxon specific primers and PCR conditions for the Harpiniinae MIWA specimens which were not successfully sequenced with the Universal primers. As a starting point, an additional 13 MIWA specimens had tissue extracted for DNA, and then dissected and permanent slides were made in order to morphologically score them. Each appendage was photographed and the images stacked. The primers and PCR conditions are a work in progress; however, this was a very successful trip resulting in a lot of data to analyse!

I also had the chance to explore the fantastic city of Bergen! I absolutely loved my time spent here- I generated a lot of data and learned so many new skills and new insight into my PhD project. Win-win! I look forward to returning again one day.

-Marla

Getting back in business

The blog has been quiet over summer – but we’ve been busy!

The #AnnelidaCourse2017 came to an end, and happy participants went back to their home institutions with a lot of new knowledge, a increased contact network, and many new friends.

a)Students working in the lab; b) Picking interesting animals from the samples onboard R/V Hans Brattström; c) Animals to be studied; d) Group photo of most of the participants; e) Detailed study and drawing of a specimen; f) Field work onboard R/V Aurelia Fotos: K.Kongshavn (a,b,e), G. Kolbasova (c), G.Jolly (d), S. Rosli (f)

a) Students working in the lab; b) Picking interesting animals from the samples onboard R/V Hans Brattström;
c) Animals to be studied; d) Group photo of most of the participants; e) Detailed study and drawing of a specimen; f) Field work onboard R/V Aurelia Fotos: K.Kongshavn (a,b,e), G. Kolbasova (c), G.Jolly (d), S. Rosli (f)

Heaps (HEAPS!) of samples have been cataloged and labeled, DNA-sequencing has completed on the shipment we sent in June and we’re working on analyzing the results, and samples from the cruises we particpated on have and are being sorted.

The next shipment of animals to be barcoded through NorBOL is being assembled – of marine invertebrates from our collections, one plate of polychaetes and one plate of isopods have been prepared, and we plan on completing a few more plates before shipping in October.

Isopods for barcoding - these have all been collected and identified by the MAREANO project. Photo: K.Kongshavn

Isopods for barcoding – these have all been collected and identified by the MAREANO project. Photo: K.Kongshavn

We will also get contributions from several of the Norwegian Taxonomy Initiative projects (Artsprosjekt) that are running, and a plate with insect samples made by the students of BIO233 (I was down there today giving them an introduction to barcoding, NorBOL and the BOLD database) – hopefully we’ll get good results on all of it.

-Katrine

Fieldtrip to Taiwan: sampling on the periphery of the coral triangle

As part of our research programme to study “opisthobranch” molluscs in the Indo-West Pacific and understand the drivers of present diversity and biogeography on this region, we carried out a 3-week fieldtrip to Taiwan during May 2017. Taiwan is located in the China Sea north of the Philippines on the periphery of the “coral triangle”, the richest marine hotspot in the world contained within Indonesia, Papua New Guinea, and the Philippines.

Goniobranchus kuniei. Longdong, NE Taiwan

Goniobranchus kuniei. Longdong, NE Taiwan

Although situated outside this hotspot, Taiwan is influenced by the warm water Kuroshio Current flowing from the Philippines along the Luzon Strait and striking the southern part of Taiwan where it splits in two branches which drift northwards along both the eastern and western coastlines of the country. This confers to Taiwan tropical characteristics on its southern regions with occurrence of vast and diverse coral reef systems, while the northern coasts are of sub-tropical affinity with waters up to five degrees cooler. This combination of different oceanographic and climatic features, result on the occurrence of an extremely diverse marine fauna with different ecological requirements.

To cover different oceanographic regimes in the best possible way within our limited timeframe, we visited three regions for about one week each.

We first sampled along the southern tip of Taiwan at the Kenting National Park together with Professor Chung-Chi Hwang from the National University of Kaohsiung.

The sampling team-at-Kenting-left-to-right-Trond-Oskars-Wei-Ban-Jie-Chung-Chi-Hwang-Manuel-Malaquias

The sampling team at Kenting. left to right: Trond Oskars, Wei Ban Jie, Chung Chi Hwang, Manuel Malaquias

Here are some of the animals we encountered at Kenting:

Who are you?

Who are you?

The second week was dedicated to the off shore island of Penghu in the Strait of Taiwan where we have worked together with Professor Yen-Wei Chang and his students from the National Penghu University of Science and Technology.

A happy party of sea slug hunters in Penghu, Taiwan

A happy party of sea slug hunters in Penghu, Taiwan

The garage of our hostel in Penghu, transformed into a wet lab for a week

The garage of our hostel in Penghu, transformed into a wet lab for a week

Goniobranchus cf. sinensis

Goniobranchus cf. sinensis

Hypselodoris maritima

Hypselodoris maritima

A beautiful flatworm

A beautiful flatworm

Finally, we sampled on the NE coast along the Longdong area in collaboration with Dr Vincent Chen and Dr Wei-Ban Jie, the first an authority on Taiwanese coastal ecology and the latter the author of the book “Taiwan Nudibranchs”.

A glimpse of the beautiful waterscapes at Longdong, Taiwan

A glimpse of the beautiful waterscapes at Longdong, Taiwan

Phyllidia ocellata Longdong, NE Taiwan

Phyllidia ocellata Longdong, NE Taiwan

Thuridilla sp. Longdong, NE Taiwan

Thuridilla sp. Longdong, NE Taiwan

Halgerda carlsoni Longdong, NE Taiwan

Halgerda carlsoni Longdong, NE Taiwan

Shallow habitats between the tidal zone down to 30 m deep were surveyed for “opisthobranchs”, and at the end we estimate to have collected a staggering 140 species.

The samples are now under curation and will soon be integrated in the systematic collections of the Natural History Museum of Bergen, becoming available for scientific study.

-Manuel Malaquias, Natural History Museum of Bergen, UiB

Update from the Annelida-course

20170609_100827

As told last week, we are currently hosting the international course on Annelid Systematics, Morphology and Evolution at the University of Bergen’s field station. Here’s a little update of what we have been up to since the previous post:

The days are pretty packed, with lectures, sampling, and lab work – thankfully both students and teachers are enjoying the work, and the mood in the lab is sunny (even if the Bergen “summer” is somewhat…fickle these days). We have covered a multitude of research topics, methods,  habitats, and annelid groups so far, with still more to come.

Happy, hard working  students in the lab

Happy, hard working students in the lab

"summer" sampling - we did get very nice samples!

“summer” sampling – we did get very nice samples!

Back in the lab, Torsten explaining todays exercises

Back in the lab, Torsten explaining todays exercises

Mixing the solution to get the tiny annelids out

Mixing the solution to get the tiny annelids out

The jaws of a small Ophryotrocha

Pointing out the jaws of a small Ophryotrocha

We’ll keep blogging from the from the course, so check back!

You can also get some glimpses of the exciting world of Worm researchers (!) by checking the tag #annelidacourse2017 on Twitter (you don’t need an account to do that, just click the link).

Congratulations to our latest PhD!

Freshly minted PhD!  (photo: Kenneth F. Bosch)

Freshly minted PhD!
(photo: Kenneth F. Bosch)

Andrea successfully defended her Ph.D. thesis “Dietary specialization and molecular phylogeny of the family Aglajidae (Cephalaspidea: Gastropoda) with species delimitation analysis and biogeography of two genera from the clade Chelidonura sensu lato” earlier today. She was supervised by Manuel A.E. Malaquias from the Department of Natural History, UM, and Henrik Glenner from the Department of Biology.

You can read more about her work here (in Norwegian)

Congratulations and all the best wishes from us!

Below are photos of some of the species, if you are wondering how they look (pics by Manuel)

Full house!

Busy workers

Busy workers

The lab is teeming with guest researchers these days, as we have these three lovely polychaetologists visiting to work on the MIWA (Marine Invertebrates of Western Africa)-material.

From the left we have Kate from Wales, Lloyd from Ghana, and Polina from Russia

From the left we have Kate from Wales, Lloyd from Ghana, and Polina from Russia

Kate is working on the polychete family Magelonidae, and has written a blog post about her stay. Lloyd is working on the families Glyceridae and Goniadidae, and Polina is doing her MSc thesis on the Lumbrineridae. You can find short project descriptions of these (and many of our other) polychate projects here.

Makes sure to check by our MIWA-blog for more updates in the time to come!

Door # 18: MSc completed

Congratulations to Jenni, our (former!) master student, who presented her MSc project last Friday!

She has been working on the phylogenetic systematics and evolution of a genus of small marine gastropods called Phanerophthalmus, and she’s done an impressive amount of work.

Phanerophthalmus crawling on seagrass. Photo: M. Malaquias

Phanerophthalmus crawling on seagrass. Photo: M. Malaquias

 

The project was titled
Systematics, biogeography, and trophic ecology of the genus
Phanerophthalmus A. Adams, 1850 (Mollusca, Cephalaspidea, Haminoeidae) in
the Indo-West Pacific, and was supervised by Manuel Malaquias.

Celebrating our freshly minted MSC with coffee, cakes and bubbles

Celebrating our freshly minted MSC (second from the left in top photo) with coffee, cake and bubbles!

We wish you all the best, Jenni!

Door #17: New master student

Polina

Polina

Polina Borisova, a first year master student from the Zoological Department of the Moscow State University (Russia), is coming to the Invertebrate Collections of the University Museum of Bergen with a 1-month research visit in January 2017.

Polina is going to work on the bristle worms from the family Lumbrineridae studying the collection from West Africa and Norway. Her project is jointly supervised by Dr. Nataliya Budaeva from the University Museum of Bergen and Dr. Alexander Tzetlin from the Moscow University.

Various Lumbrineridae from West Africa, scale 1 mm (Photos from BOLD).

Various Lumbrineridae from West Africa, scale 1 mm (Photos from BOLD).

Lumbrineridae are the worms with relatively poor external morphology but complex jaw apparatus. The structure of jaws has been traditionally used in the systematics of the family in the generic diagnoses. Polina is utilizing the methods of microCT to study the jaws of lumbrinerids in 3D.

Jaws of Scoletoma fragilis from the White Sea scanned using microCT showing ventral solid mandibles, forceps-like maxillae I and denticulate maxillae II and II, carriers of maxillae are omitted (Photo: P. Borisova)

Jaws of Scoletoma fragilis from the White Sea scanned using microCT showing ventral solid mandibles, forceps-like maxillae I and denticulate maxillae II and II, carriers of maxillae are omitted (Photo: P. Borisova)

Polina is also going to sequence several genetic markers to reconstruct the first molecular phylogeny of the family. This will allow testing the current hypothesis on the intergeneric relationships within Lumbrineridae and will aid in tracing the evolution of jaws within the family.

-Nataliya & Polina