Category Archives: new species

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

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!

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!

New species of West African snails

Our studies of mollusks have revealed new species of philinid snails. They are described in a paper that was published today in the Zoological Journal of the Linnean Society with open access: http://onlinelibrary.wiley.com/doi/10.1111/zoj.12478/full

We used both morphological techniques and DNA-based species discrimination methods in this study and DNA-barcodes have been uploaded to the BOLD-database. Laona nanseni was named as a tribute to the Nansen programme and Philine schrammi in honour of J. R. Schramm, who founded JRS Biodiversity Foundation, an important sponsor of our work.

Laona nanseni new species

Laona nanseni new species

Philine schrammi new species

Philine schrammi new species