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Tools of the trade – the BOLD database

One of the topics covered in depth during the workshop is the selection of specimens and the preparation of tissue-samples. These will to be sent for DNA sequencing, and the genetic sequence will then be included in the Barcode of Life Data Systems (BOLD). The aim is to obtain standardized genetic sequences (“barcodes”) for the various taxa that we are working on. The barcode 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.

There is a very real challenge connected with estimating biodiversity when many of the species are still undescribed, as is the case with many invertebrate species, 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 low.

We have not yet received any barcodes for our MIWA project, but the project page on BOLD is getting populated with images and geographical information.

Uploading pictures

Uploading pictures

Brittle star image gallery

Brittle star image gallery

Crab image gallery

Crab image gallery

This picture shows a plot of crab species that have been DNA barcoded around the World. Notice the lack of records from West African waters.

This picture shows a plot of crab species that have been DNA barcoded around the World. Notice the lack of records from West African waters.

This picture shows how we are presently about to add records of about 60 crab species to the BOLD database.

This picture shows how we are presently about to add records of about 60 crab species to the BOLD database.

 

How is it that the polymerase chain reaction (PCR) can make numbers of copies of a piece of DNA?

How is it that the polymerase chain reaction (PCR) can make numbers of copies of a piece of DNA? (Slide from an intro to the technology of PCR and Sanger sequencing given by EW.)

Lecture about the correct procedure for tissue sampling

Lecture about the  procedure for tissue sampling and recording of data for the BOLD system

The specimens from whuch we take the DNA tissue sample is documented through photographs

The specimens from which we take the DNA tissue sample is documented through photographs

A completed microplate with 95 tissue samples

A completed microplate with 95 tissue samples

Sorting the snails

Mollusca sorted for species identification

Mollusca sorted for species identification

When samples are sorted to main groups of taxa,  individuals can also be separated into “morphotypes” based on their general appearence, Morphotypes may or may not correspond to species and this has to be decided by more thorough examination for species identification.

A sample from an epibenthic sled

Different sampling tool are available for sampling animals. They will retrieve different parts of bottom fauna, depending also on factors such as net size, cruise speed, and the size and agility of the animals. An epibenthic sled can catch the animals that live on or just above the bottom surface. This sample on a sieve contains snails (Mollusca, Gastropoda), brittle stars (Echinodermata, Ophiura), polychaete worms (Polychaeta), shrimps, crabs and hermit crabs (Crustacea, Decapoda).

A sled sample from 30 m depth off Senegal.

A sled sample from 30 m depth off Senegal.

Temperature towards the deep waters

Annual surface temperature  according to oceanographic data in World Ocean Atlas (WOA09)

Annual surface temperature according to oceanographic data in World Ocean Atlas (WOA09).

Oceanographic data are showing hight temperatures in the tropical surface waters. However, the striking geographical differences become less when the measurements are taken in the deeper parts of the water column. Click this link to see a rough picture of how temperature changes towards the deeper layers.

(The animation was made by EW with Reiner Schlitzerands ODV and converted to a Windows Video File.)