Author Archives: katrine

Indeed we did!

(get DNA from our faded stars, that is)
zmbn_115365_1

As explained in a previous post, we submitted tissues samples from the sea stars (class Asteroidea) that were suitable for DNA-analysis to the CCDB lab and the BOLD database. We just recieved the preliminary results, which are very promising!

The next step now will be to collaborate further with our asteroid taxonomist, and evaluate the genetic data combined with traditional morphology based taxonomy. Combining barcoding and morphology in this way helps us explore and understand the biodiversity better.

Stay tuned for updates!

Cataloging: the art of keeping track

Combining a multitude of guest researchers and our own efforts at working through the material, we’re producing thousands of new records to be cataloged into our database (we’ll get those listed here eventually, work is still ongoing at the moment).

Cataloging samples also means that the material needs to be physically updated;
New labels are printed for the samples,  and these must then be matched to their respective jars, inserted, and stored safely. It may sound pretty straight forward, but with this many samples, it is still a time consuming job.

 

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: http://miwa.b.uib.no/allprojects/polychaeta-projects/

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.

Guest researchers: Lloyd

Further investigations of the diversity of the Glyceriformia (Polychaeta: Goniadidae and Glyceridae) from West African shelf areasimgp1313

For the past three weeks, Lloyd, who is a Senior Environmental Scientist at Envaserv Research Consult in Ghana, has been visiting us to continue work on the project we have running on the Glyceriformia in the MIWA-material. This project was initiated when Lloyd and Willams were here visiting in November 2015. They worked closely together with Tom, using the available literature to identify and select animals for barcoding, and to get a feel for the diversity of the group.

Similar projects on other polychaete families have taught us that the current knowledge of species diversity and distribution of the region is not comprehensive – there are more species than what is currently described in the literature, so we attempted to barcode representatives of all the morphologically distinct groups – it’s highly likely that material contains species that are new to science.

From this work, 19 “species” were identified based on morphology, and several representatives for each were selected for genetic barcoding: A voucher specimen is selected, photographed, and tissue sampled. The tissue sample is sent to the CCDB lab in Canada for sequencing, whilst the photo and metadata (such as where the animal was collected, who has identified it, at which institution is the voucher specimen stored etc.) is uploaded to the international database named BOLD – Barcode of Life Datasystems, as part of the iBOL (international barcode of life) initiative.

Unfortunately, only 50% of the specimens we tried to Glyceriformia©University_Museum_of_Bergenbarcode resulted in a barcode sequence, but even so the DNA indicated 21 genetically distinct groupings (“BINs”).

Last summer we made a poster summarizing the work we had done, and presented it as a poster at the 12th International Polychaete Conference in Wales in August 2016.

We’ve continued the work, both with sorting more samples, thus making more material available for studies, and by doing detailed examinations of the specimens we have. This is done using both regular light microscopy and scanning electron microscopy (SEM).

Some of the characters that needs examination - overall morphology, jaw structures, parapodia and bristles, and the papillae on the probocis

Some of the characters that needs examination – overall morphology, jaw structures, parapodia and bristles, and the papillae on the proboscis

Discussing the results from the previous round of barcoding - where do we need more data?

Discussing the results from the previous round of barcoding – where do we need more data?

Tom and Lloyd working on taking tissue samples

Tom and Lloyd working on taking tissue samples

During his most recent stay, Lloyd continued the work with identifying animals and selecting specimens that we will submit for barcoding – we’ll try to get the next plate sent in by the end of the month, and hope for a high(er) success rate and further insights in the diversity of the Glyceriformia of the region.

Thank your for visiting, and for all your hard work, Lloyd! We hope to see you again soon.

Guest Researchers: Kate

Kate, from Amgueddfa Cymru – National Museum Wales, has been back visiting us, and is giving us an update on how the work on the magelonid project is coming along

The shovelhead worms

– taxonomy of magelonid polychaetes – an update

16th – 27th January 2017

Kate hard at work studying the MIWA material

Kate hard at work studying the MIWA material

I came to the University Museum of Bergen (UMB) back in November 2015 to work on shovelhead worms (Magelonidae) collected as part of the MIWA-project. In particular, the priority was to select specimens for DNA sequencing from each of the putative species that had been identified whilst studying the material back at the National Museum Wales in Cardiff.

 

Studying the results from the first round of sequencing

Studying the results from the first round of sequencing

Some of the DNA voucher specimens

Some of the DNA voucher specimens

 

The initial results came back with sequences from 45 of the 72 tissue samples that were taken, mostly from the MIWA project but also European magelonid samples for direct comparison. The corresponding tree showed some interesting results and included sequences from 13 of the 20 putative species that had been highlighted previously. However, sequences from the other species identified, and further sequences from those species that only had one or two were still needed.

So work continued back in Wales, looking for further specimens for sequencing. However, it was felt that it would be beneficial to come back to Bergen in order to further study the DNA voucher specimens that had sequences already, comparing them morphologically to new material selected. It was also hoped to select alternative specimens for sequencing which had previously failed.

Sometimes magelonids can be pretty small

Sometimes magelonids can be pretty small

So, I travelled back to UMB in January 2017, just in time to catch the end of the snow, before the rains came again to spend two weeks studying MIWA material. Each of the DNA Voucher specimens were studied in great detail, making detailed notes, drawings and full taxonomic descriptions of each.

Each of the DNA voucher specimens was carefully studied taking detailed notes and making drawings of each

Each of the DNA voucher specimens was carefully studied taking detailed notes and making drawings of each

This enabled the selection of further specimens of the same species for sequencing but also highlighted specimens that showed differences. Consequently 74 additional specimens have now been chosen for sequencing. These have all been photographed and are now ready for tissue sampling before being sent off to Canada for sequencing.

Whilst those samples are being sequenced, the process of drawing, imagining, measuring and describing each species will begin back in Cardiff with formalin fixed samples.

With so many potential new species, this could be quite a lengthy process but luckily some of this work has already started. Work commenced looking at the more stout species within samples. These species usually posses a pigment band in the posterior thorax and unlike most magelonids are known to build sediment tubes. Until now only one species with a pigment band has been described from African waters, Magelona cincta, Ehlers, 1908 from Algoa Bay, South Africa. However, a further five species with pigment bands have been found in the MIWA material, four of which are believed to be new to science. Full taxonomic descriptions and a key to these species have already been produced and the process of imaging and drawing these will begin in Cardiff next week.

One of the species with a thoracic pigment band

One of the species with a thoracic pigment band

Now the process of waiting for the sequences begins and wondering if it will throw any surprises into the ring. So back to Cardiff armed with two notebooks full of notes and drawings (and three less pencils!) ready to being drawing and describing.

-Kate

Thank you for visiting (always a pleasure!), and best of luck with the myriad of new species!

Will we get DNA from our faded stars?

We have done substantial amounts of COI barcoding on various animal groups through the MIWA-project. You can find all the specimens that we have submitted for barcoding here. Of the Echinodermata we have previously submitted Echinoids (sea urchins) and Ophiuroids (brittle stars). Currently we are focusing on the class Asteroidea, the sea stars.

There were not terribly many sea stars in our material, and all of the Asteroids were identified when we had asteroid specialist Anna Dilman visiting last spring.

Part of this material is fixated in ethanol and therefore available for genetic work, and we’ve been waiting for some more material to come along so that we would have enough samples to fill the 95 wells in a plate for barcoding and uploading to the BOLD-database. Now we’ve gotten some supplemental material, and are preparing a plate of mainly Asteroidea. We are also including a few brittle stars, as we had six Gorgonocephalidae (basket stars) waiting to be barcoded, and they are plain too cool to pass up. We did a blog post about basket stars in our InvertebrateCalendar, click here to read more about the head of the Medusa.

Why “faded”? Well, in real life they are amazingly beautiful critters, looking something like this:

By Philippe Guillaume - Flickr, CC BY 2.0, https://commons.wikimedia.org/w/index.php?curid=29948486

By Philippe Guillaume – Flickr, CC BY 2.0, https://commons.wikimedia.org/w/index.php?curid=29948486

But once a specimen of the same species – this is a Astropecten aranciacushas been dragged up by a trawl and marinated in ethanol for a while, it looks  more like this:

Astropecten aranciacus from Sao Tome & Principe, collected at 54 m depth

Astropecten aranciacus from Sao Tome & Principe, collected at 54 m depth

Thankfully, the colour loss does not mean that the animal is “ruined” – it still retains its key identifying characters and DNA – they just looks a bit less exiting for us non-sea-star-experts!

The cast of characters so far - there's a few waiting to be photographed still

The cast of characters so far – there’s a few waiting to be photographed still

We’ll finish in the “photo booth” and get the tissue sampling done over the next couple of days, and hopefully our faded stars will shine (as barcode vouchers) after all!

Stay tuned for updates.

Guest researcher: Mario

Mario

Mario

Mario (who also visited us in January) came back to continue his work on the Terebellids and Pista (polychaeta) in October. In his own words: This time, I take to my home two papers close to completion; one about species of the genus Pista (Terebellidae) with additional information to what I found during my last visit in January. The second paper is about species in the subfamily Polycirrinae (Terebellide) from the West coast of Africa.

Pista cristata

Pista cristata

The idea is combine drawings, digital photos of specimens with methyl-green staining pattern and SEM pictures, as well as molecular information that will hopefully help us separate species and make better estimates of the region’s biodiversity.

You can read more about Mario’s visit in our Invertebrate Advent Calendar, which is running from December 1-24th on our collections blog. Click here to find all the calendar posts!

Guest researchers: Andres

Andres_photoWe recently had Andrés Arias from the University of Oviedo, Spain, visiting our lab to work on the MIWA-material, and asked him to share a little about his work. In his own words:

During my visit to the Bergen Museum I studied two genera of onuphid polychaetes, Onuphis and Mooreonuphis collected by the MIWA Project in West Africa.

 

The taxonomy of eastern Atlantic species of the genus Onuphis has been confused due to the somewhat cursory and misleading descriptions of species as well as the disregard of the true identity of the type species of the genus. Recently this confusion began to clear as a result of more detailed morphological studies and the formal redescription of the controversial type species, O. eremita. I have been working on European and Mediterranean Onuphis as well as intertidal/shallow subtidal Onuphis spp. and Mooreonuphis spp. from West Africa and the Macaronesian archipelagos.

Onuphis_MIWA

Worms from the genus Onuphis

Now, I’ve had the great opportunity to start working on deeper samples of Onuphis and Mooreonuphis from W. Africa. The study of this material is very exciting and promises to be very interesting since in a first approximation we have found at least six species that are new to science! This will contribute to updating the list of bristle worms from West Africa. This information will fill spatial gaps for the genera Onuphis and Mooreonuphis, in a region where little information is available, which is undoubtedly needed!

I would like to thank everybody at the Museum for their kindness and help, which made my stay very pleasant!

Thank you for visiting, and for contributing to the blog!

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.