Category Archives: Crustacea

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

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.

Preparing plates

Today, the mail brought us this:

New plates for tissue samples!

New plates for tissue samples!

A good thing too, as we were running out of plates to fill. We are currently busy preparing four (possibly five) plates of material from the west coast of Africa.

There will be one plate of Amphipoda, which we have not submitted from this region previously (resulting from the workshop that Anne Helene and Ania had in December).

The remainder of the shipment will be polychaetes that have been identified both by our resident taxonomists and the guests that came here to work on the material over the past couple of months; São, Julio, Kate, and –most recently – Mario.

Mario at work in the lab

Mario at work in the lab

Mario arrived here on the 4th of January, and stayed for a month – we’ll make a proper post about his work here in a bit (he is currently on his way to field work in the Antarctic, but has promised a post later on). His main field of interest are Terebellomorph polychaetes, and he focussed especially on the genus Pista during his stay.

So now we are working on organizing, photographing, cataloguing and otherwise preparing the material – our guest have been busy, so there is a wealth of new data to deal with.

Tools of the trade

Tools of the trade

Tom taking tissue samples for two plates of Ampharetidae and other Terebellomorph polychaetes

Tom taking tissue samples for two plates of Ampharetidae and other Terebellomorph polychaetes

Photos and data entry

Photos and data entry

We have new guests arriving in a few days; there’s plenty to do. Stay tuned for updates!

Let’s hope for successful sequencing and many interesting results!

PS: make sure to check invertebrate.w.uib.no this Friday (the 12th) for some Biodiversity Love; the JRS Biodiversity Foundation has asked us to

Please share your love of biodiversity this Valentine’s Day with the hashtag #bdvalentine. Have fun and help raise awareness of biodiversity and conservation!  This is a chance to draw your audience to your social media and to express appreciation for your partners, grantees, collaborators, or someone you love.”

We are joining in, don’t miss out!

#bdvalentine

Presentation at the 8th International Crustacean Congress (ICC-8)

Almost 300 researchers from many nations were convened last week at the beautiful Campus Westend of the Goethe–University in Frankfurt for the 8th International Crustacean Congress (ICC-8). Many interesting talks and high quality posters were presented over six days. A special workshop on DNA-identification and barcoding filled the auditorium to the the edge and left many attendants standing through the session. EW gave a 15 minutes talk on results from our barcoding of decapods and stomatopods. He particularly emphasized how barcoding can reveal discordant species identifications among different labs and research environments and pinpoint the need for reidentification and / or taxonomic revision of species.Copy of GoetheUnivFrankfurtICC-8_presentation

The Casino building of the Goethe University

 

 

 

A left-handed hermit

Ciliopagurus caparti belongs to the group of hermit crabs that is sometimes called left- handed because the left claw is larger than the right, as opposed to the situation in other hermit crabs. C. caparti was originally described as a new genus Trizopagurus. The original description in Bulletin, Institut Royal des Sciences Naturelles de Belgique, 28(39): 1–8 is available for download from ATOL:Decapoda. We hope that our just submitted samples will yield DNA-barcodes of the species in the BOLD database.

Ciliopagurus caparti expelled from its snail shell residence

Ciliopagurus caparti expelled from its snail shell residence

Geographic position of a new sample to the BOLD-database

Geographic position of a new sample to the BOLD-database

 

Slipper lobster

I just photographed some specimens from the family Scyllaridae, and they are such funny looking critters that I decide to share them on the blog. The Scyllaridae are found in all warm oceans and seas, and typically live from shallow water and down to depths of about 500 m (according to Wikipedia).

Scyllarus carpati from Mauritania

Scyllarus carpati from Mauritania

Pictured is a Scyllarus carpati from Mauritania, collected by sledge at 100 meters.

If you click here, you can se the distribution of the species, as well as its IUCN Red List status. We will take tissue samples from this specimen and send it for COI DNA barcoding, which will be incorporated in the BOLD database. There are records of specimens from the same genus recorded in BOLD already, but none of this particular species, as you can see if you search for Scyllarus carpati here.

Portrait of a crab

Sakaila africana was recognized as a new species by Raymond B. Manning and L.B. Holthuis in 1981. Their publication in The Smithsonian Contributions to Zoology is an important source  to the identification of West African crabs. An electronic version of the publication is available on this link. Our workshop found Sakaila africana in samples from Guinea Conakry.

Sakaila africana

Sakaila africana