Author Archives: katrine

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 – further news
11th – 22nd February 2019

For those not familiar with magelonids, they are magnificent marine worms with shovel-shaped head regions which are utilised to dig in soft sediments. There are approximately 72 described species (many of which live in shallow water up to several hundred metres deep. Although there are magelonid species described from many parts of the world there are several regions which we know relatively little about; those of the western coast of Africa virtually nothing. With that in mind I started investigating the magelonids from the MIWA project back in 2013 and made my first visit to the University Museum of Bergen to look at the material in November 2015 and a second trip in January 2017.

Where magelonids are present you often find a huge diversity of species, with 6-10 species within a region not uncommon. However, the diversity of magelonids off the western coast of Africa has been extensive and we believe that there are in excess of 20 species within the sampling area (Morocco-Angola).

So, we have been working our way through the extensive collection of material from MIWA, identifying, describing, drawing, photographing and cataloguing all the shovelhead worm species. Alongside morphological investigations, we have taken many samples for DNA barcoding (CO1, 16S and 28S), thus allowing us to produce phylogenetic trees. With so many species and specimens to deal with, we felt it prudent to publish the results in a series of papers. To start the process, we decided to concentrate on the species that carry pigmentation in the posterior thorax. These are generally stout, short species, with short ‘frilly’ palps, and are known to construct distinct sediment tubes. One species within this group is Magelona cincta Ehlers, 1908 first described from South Africa. Normally, within a region you generally only find one or two species carrying these distinct pigment bands. However, we have found six species, five of which are new to science. Since my last visit all six of these species have been described and illustrated and the first paper on MIWA magelonids is complete and will be submitted in due course. Phylogenetic analysis has shown this group to be monophyletic.

MIWA shovelhead worm with distinct crenelated horns

For the next paper we are focusing on a group of magelonids that have horns on the top of their head region. These may be crenulated with distinct triangular points along the anterior margin, or may be entirely smooth. Similar species are Magelona crenulifrons Gallardo, 1968 (from Viet Nam), Magelona cornuta Wesenberg-Lund, 1949 (from the Gulf of Iran), and Magelona lusitanica Mortimer, Gil & Fiege, 2011 (from Portugal). There are five species within the MIWA material, three of which are fairly common but two of which we have only a few specimens of. The focus of this trip is to look for further specimens of those species that we have limited material of, which will help us to provide more fuller descriptions of the species.

So, we hope that by the end of my time here at UiB, we will have almost completed the descriptions of the ‘horned species’. The next step is to analyse more DNA samples, which will be done here in Bergen and I will return back to Cardiff in order to draw and photograph the five species ready for publication. Due to the huge diversity of species, it is a long process. However, by the time we have finished we will have a comprehensive understanding of the shovelhead fauna of Western Africa. Whilst many of the species have limited species ranges, we have seen an overlap with European faunas and some species with large distributions.

-Kate Mortimer-Jones

 

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!

-Marla

DNA-barcoding: update

Yesterday, Endre and I attended an event where the different units of the University of Bergen were invited to  “..present ongoing digitalisation projects, tools and methods, and future digital solutions.”

We brought with us a poster titled “Data con carne – sources of new knowledge on biodiversity” (in Norwegian), where we presented how our barcoding efforts on both African and Norwegian material are parts of a global undertaking of building a “library of life”, and how using huge databases such as BOLD can help us gain better understanding of biodiversity – and on where to focus our efforts in unraveling the taxonomy.

2017_digital-day

There is a very real challenge connected with estimating biodiversity when many of the species are still undescribed, as is the case with many invertebrates, especially the more obscure and diminutive groups.  In such cases, barcoding can serve as a tool in screening for biodiversity, and aid the taxonomists in identifying areas where the taxonomic resolution is poor.

There is a global effort underway to establish a library of short,  species specific genetic sequences. These standardized genetic sequences (“barcodes”) consists of a segment of approximately 650 base pairs of the mitochondrial gene cytochrome oxidase c subunit 1 (COI). You can read more about DNA barcoding on WIKIPEDIA.

For MIWA, we have submitted over 2700 tissue samples from over 600 morphospecies for DNA barcode sequencing through the BOLD-pipeline, where the lab work is done in Guelph, Canada, and the data is uploaded to the Barcode of Life Data Systems (BOLD Systems) .

Out of these, 1450 sequences have been obtained (54% sequencing success rate), and these cluster into close to 550 BINs (OTUs) – suggesting that the diversity may be (much!) higher than what our preliminary investigations reveal. This is not so surprising, considering how hugely diverse and little studied the invertebrate fauna of the GCLME and the CCLME is.

Below is an interactive map of the submitted samples, you can click on the stations to see the specimens that have been sent from that location, and whether or not they have gotten a barcode. You can also follow this link to find the map

What we find is that it is crucial to be able to go back and reexamine the material post-barcoding, and that is where the “con carne” part of our poster came from;

Our barcoding revealed several examples of mismatching taxonomic identifications amongst researchers in different labs and institutions in different countries. This illustrates a major challenge, as it has been shown that when benthic fauna is used in standardized methods for quality assessment and monitoring, mismatching identifications produced by different identifiers can have strong effects on indexing and valuation of ecological conditions in the same habitat.

For DNA barcoding to be useful, it is absolutely neccessary that the correlation between species name, specimen, and barcode is correct (or at least as close to it as we can get, if the species is undescribed).

We must first build this reference library before barcoding can be reliably used for identification of unknown organisms. Hence it is imperative that the voucher specimens that correspond to the genetic barcodes are deposited in a museum where it will be preserved and made available for research.

-Endre & 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.w.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 aranciacus – has 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.