Category Archives: student projects

Guest researcher: Sara Castillo

“Opisthobranch” gastropods from West Africa

Dr Sara Castillo  has recently finished her PhD (September 2017) with a thesis on the taxonomy and diversity of gastropods and bivalves from North-west Africa (Morocco to Sierra Leone), based on material collected during cruises of the Norwegian and FAO Nansen Programme and other scientific projects.

The Natural History Museum of Bergen has since 2005 collaborated in the benthic sampling of the Nansen Programme, and between 2013–16 the Museum was awarded funding from the American JRS Biodiversity Foundation to aid on the study and DNA barcode of the western African invertebrate benthic fauna. During this period Sara visited Bergen to participate in a workshop on to the taxonomy of western Africa bivalves organised by the Museum. The “opisthobranchs” gastropods (sea slugs and other related lineages) were not covered by Sara Castillo’s research and in Bergen we have so far only studied in depth the philinid snails (fam. Philinidae sensu lato).

Sara is visiting the Museum for 6-weeks (1st Nov–15th Dec) to study both ours and the University of Vigo’s collection of opisthobranchs from West Africa. Representatives of all morphotypes will be DNA barcoded and identified to species level. Because of its diversity and difficult taxonomy in western Africa the nudibranch family Arminidae will receive special attention and the barcoding work will be complemented with anatomical characterization of species backed by scanning electron microscopy. Our goals are to produce an inventory of the West Africa “opisthobranchs” collected during the Nansen programme and a taxonomic review of arminid nudibranchs from the region.

Guest researcher: Marla Spencer

Ready for fieldwork!

Marla, a PhD student supervised by Dr Tammy Horton (NOC), Dr Andrew Gates (NOC), Dr Lawrence Hawkins (UoS), Dr Miranda Lowe (NHM) and Dr Gordon Paterson (NHM) has spent 6 weeks in the invertebrate collections at UiB.


Marla was studying the 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.

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 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

Harpinia abyssi Photo: M. Spencer

Out of the 2700 tissue samples, a total of 1450 sequences were obtained (54% sequencing success rate). This is not uncommon as the ‘Universal’ barcode protocol often needs to be adapted for different taxon groups.

At work in the DNA lab


Working with Anne Helene within the molecular biology labs at the University of Bergen, currently developing 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, then dissected and permanent slides were made in order to morphologically score them. Each appendage was photographed and the images stacked. At this time the primers and PCR conditions are a work in progress, but we will keep you posted. However, this was a very successful trip resulting in a lot of data to analyse!


Guest researchers: Polina

Polina, a master student jointly supervised by Dr. Nataliya Budaeva (UiB) and Dr. Alexander Tzetlin (Moscow State University) has spent a month in the invertebrate collections studying the bristle worms from the family Lumberineridae from the Western African Waters.

Lumbrinerid genera can be distinguished by the morphology of the jaw apparatus consisting of ventral fused mandibles and two rows of dorsal maxillary plates. Polina learned how to dissect the jaws and identified at least 11 genera of Lumbrinerids from the studied material. She is also planning to used microCT back at the Moscow University to study the morphology of the jaws in 3D. During her stay, Polina has studied the composition and morphology of chaetae, another character used in generic and species identification in Lumbrinerids, using SEM.

In addition, all studied specimens will be used in the molecular analysis to reconstruct the first phylogeny of the family Lumbrineridae based on genetic data. Please see the full description of the project:

A – Ninoe sp. anterior part of body, ventral view; B – the same, close view of parapodia and chaetae; C – Gallardoneris sp., compound hooks; D – Scoletoma sp., anterior part of body.

Scanning Electron Microscope (SEM) images of Lumbrinerids: A – Ninoe sp. anterior part of body, ventral view; B – the same, close view of parapodia and chaetae; C – Gallardoneris sp., compound hooks; D – Scoletoma sp., anterior part of body.

Mapping our barcoding efforts

Here is a  interactive map of all the samples (2175 as we speak!) that we have submitted to the BOLD-database for genetic barcoding.

You can also  follow this link to find it.

miwa stations

All the stations from which we have submitted specimens for barcoding

By clicking around on the map you can see how many specimens we have submitted from each station, as well as photos of the animals and wether or not the sequencing was successful and resulted in a genetic barcode.

zoomed in

By clicking on a station, you get the information about which animals have been sequenced – here two brittle stars that were both successfully barcoded











The samples we have submitted (so far – there are still plans to do more!) include several animal main taxa; Crustaceans, Echinoderms, Molluscs and Polychaetes. These animals have been sorted out and identified by employees at the invertebrate collections, and by visiting guest researchers who have come here to work in the material – so it is very much a combined effort behind this.

# of submitted specimens (animals) from each phylum

# of submitted specimens (animals) from each phylum

Not all our material is suited for genetic analyses; fixation in formaldehyde gives well preserved specimens that are well suited for morphological examinations – which is the backbone of taxonomy – but it distorts the DNA so that the samples are not eligible for molecular work.
Provided that the material has been fixated in a DNA-friendly way (i.e. in ethanol), there is a lot of work to be done before we are left with identified specimens. We wrote a bit about the sorting of samples her: “biodiversity in a dish”.

We are still working actively with this material and with the results we are getting – some of it has already been published – se our list of publications here – and more is on the way.

Studies of Hydrozoa

hydro_peopleThe first weeks of July have been dedicated to the collections of Hydrozoa.  Although the species that is presently  known as Sarsia tubulosa has been almost a totem animal to marine biologists in Bergen since Michael Sars’ pioneering studies of cnidarians and other invertebrates on the Bergen coast, this taxonomically complex group has received relatively limited attention from local students.
We are very pleased therefore that Professor Francesco Ramil Blanco and his PhD-student Marta Gil from the University of Vigo are taking the time to examine some of our material  of benthic hydrozoans. Benthic hydrozoans are sitting on various forms of substrate like sand, stones or dead shells. But many are also epibionts, which means that they are attached to other organisms such as algae, crustaceans or even other hydrozoans.

Front end of a Hyas crab carrying Hydrozoa and other organisms.

Front end of a Hyas crab carrying Hydrozoa and other organisms.

The alternation of generations between polyp and medusa stages, one of M.Sars’  discoveries, is just one of the reasons why these small cnidarians, the more inclusive group that the hydrozoans belong to, have been taxonomically challenging. There are many examples of such different life history stages having been described over time as different species.  But there are also other reasons as to why hydrozoans should be studied more thoroughly. Access to new material, better microscopes and molecular techniques are giving researchers new possibilities to assess the diversity of these strange animals.

Specimens of Hydrozoa are mounted in resinous medium for microscopy.

Specimens of Hydrozoa are mounted in resinous medium for microscopy.

Slides for microscopy

Slides for microscopy


Streptocaulus dollfusi2

Streptocaulus dollfusi – microscopy picture of part of a colony from West Africa identified by Ramil and Gil.


Team work in an enlarged micro-world

New Master thesis: studies of Diopatra polychaetes

Ongoing studies of the polychaete worms collected by « R/V Dr Fridtjof Nansen» cruises are revealing a great diversity of species including many that are also completely new to science. This observation is demonstrated in a recently completed master thesis presented by Mr Martin M. Hektoen for the Faculty of Mathematics and Natural Sciences at University of Bergen.

Mr. Hektoen decided to to respond to our announcement in 2013 of a master project and studied the genus Diopatra in the GCLME and CCLME regions supervised by Dr. Nataliya Budaeva.

Nataliya Budaeva and Martin M. Hektoen

Nataliya Budaeva and Martin M. Hektoen

He presented his work in public before the examination commission on June 26th. The thesis is begun with an opening quote from H. Hemsworth Day (1960) reading: “ … the question as to whether there is one species of Diopatra or several species is a matter of controversy.”

Hektoen’s resolution to what may now seem more as a deceased controversy is a paper recognizing nine new species of Diopatra from the East Atlantic. The studies are based on detailed morphological studies, – microscopy and Scanning Electron Microscopy, and supplemented by DNA-sequencing of mitochondrial genes. Laborious descriptions, identification keys, and a phylogenetic analysis are some of the important elements of the thesis contents.

Adjudication of the work was performed by polychaete specialist Dr Eivind Oug from the Norwegian Institute of Water Research, Grimstad, and Prof. Anders Hobæk from the Department of Biology at UiB. We extend our congratulations to Martin for his comprehensive work and fine work, and are looking forward to see the results in a peer reviewed publication in the near future. Cheers, Martin!

Participant snapshots – Trond


Name: Trond R. Oskars

Home institution: University Museum of Bergen, Norway (blog here)

What do you work with at home?

Samples, big and small

Samples, big and small

I have recently been working on preparing material for the workshop by sorting benthic samples from the West-African coast, paying particular attention to the Bivalvia (clams, oysters, cockles etc.) and the Ophistobranchs (a group of gastropods/snails), as these are some of the focus groups for the workshop.   I defined the specimens to morphospecies and/or genus, to ease the work for the experts who will be working on identifying them to species. I am also preparing papers on Cephalaspidea and Philinidae (snails) from my master thesis work, and preparing to start my Ph.D.

Jar upon jar upon jar of molluscs

Jar upon jar upon jar of molluscs

Creating some order








What are you working on here?IMG_0184

On the workshop I have been nominated as the “gastropod team”. The previous workshop got a lot of nice results on the gastropods, and it was decided to continue the work this year. My task is to organize the species by family, and pick suitable specimens from target families that we wish to do DNA barcoding on, prepare the barcoding samples, and keep the database up to date.