Author Archives: EW

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Endre Willassen Professor emeritus -zoology

Door # 8: The DNA-barcode identification machine

In a previous blog post I explained briefly how DNA-sequences are produced for the DNA-barcode library. Now I will show how the BOLD database can be utilized to identify species from sequences.

Some of the equipment used to produce DNA-sequences in our lab.

Say you have access to a lab that can produce DNA-sequences and you have a sample of a crab you cannot identify because some of the key characters are on body parts that have been broken and lost. You produce a DNA-sequence from the “barcode-gene” and open the identification engine in

Internet start window for the BOLD identification engine where you paste your unknown DNA sequence into the bottom blank window. (Click on picture to expand)

Having submitted your query to BOLD, you wait for some seconds for results. In this example BOLD returned the following window.

Example of results from a query to the BOLD identification engine. (Click on picture to expand)

The results window lists the top matches in terms of sequence similarity, and in this case we have 100 % similarity match with the crab Atelecyclus rotundatus. There is also an option to display the results as a TREE BASED IDENTIFICATION. When clicking on the option tab, the closest hits are clustered in a so-called Neighbour Joining Tree. In the window below you see parts of the tree where our unknown DNA-sequence has been joined to a group of other sequences in BOLD that have been deposited as Atelecyclus rotundatus barcodes by other biodiversity labs.

Part of TREE BASED IDENTIFICATION of an unknown DNA sequence (in red). We see that the unknown clusters with with other sequence of Atelecyclus rotundatus. The nearest neighbour branch is Atelecyclus undecimdentatus. (Click on picture to enlarge.)

The species page for Atelecyclus rotundatus gives us more information about this crab and about its records in BOLD.

Species page for the individual we identified with the BOLD identification engine. (Click picture to enlarge.)

If in fact your sequence was produced from an unknown crab, this identification seems convincing. But sometimes you should think twice about search results, and this will be the topic of a future blog post.


Door #5: DNA-barcoding with BOLD

Much of the activities in our invertebrate collections are dedicated to so-called DNA-barcoding. Our mission in the NORBOL consortium is to produce DNA-barcodes, particularly for marine fauna in Norwegian waters and to make these barcodes available with open access to records and metadata in In the same manner we have also worked to produce DNA-barcodes for marine invertebrates on the West-African continental shelf in a project called we call MIWA.

These QR-codes will take you to maps with plots of specimens that have been barcoded in our projects (or simply click on them. The red dots on the maps are interactive):

QR-code to view our barcoding efforts in NORBOL

QR-code to view our barcoding in the MIWA project

The basic idea motivating these activities is very simple in principle. You collect specimens and identify them, preferably to species, take digital photographs, and upload information about collection site and other relevant data to a database (

The specimen page has a picture and other data about the organism that the DNA sequence (presumably) was produced from (click picture to enlarge).

You take a tissue sample to extract DNA from the specimen and use DNA-sequencing technology to target a special fragment of DNA to read the sequence of nucleotides. The expectation is that this sequence may be unique for the particular species you identified.  If indeed the expectation is fulfilled, you can use that sequence as an unambiguous identifier (“bar-code”) of that species.  You have produced a DNA-barcode!

A sequence page in BOLD contains the DNA-sequence (the barcode), the aminoacid translation of the sequence, and the trace-files from the DNA-sequencing machine.(Click picture to enlarge)

Your barcode should enter a DNA-barcode library so that, with an appropriate web-interface to a powerful computer with a search algorithm that compares similarities, you should be able to search with a second sequence from another individual of the same species and find that it is identical, or at least very similar to the one you produced for the DNA-barcode library.  The benefits are potentially many. One advantage is that you may be able to identify a species although all the morphological characteristics have been lost. For the biologist DNA-barcodes may help to identify juvenile stages of a species or even the stomach contents of a predator or scavenger. For conservation, customs, trade, and food authorities DNA barcodes are a powerful means to monitor resource exploitation and attempts to swindle with species identities or area of origin of  biological products.

A taxon window in BOLD fro the crab Atelecyclus undecimdentatus. (Click picture to enlarge)

DNA-barcoding certainly also contributes to the mapping of species distributions and to survey genetic characteristics of taxa. Perhaps initially somewhat unexpected, it also reveals many problems in taxonomy that call for resolution through closer studies. More about this will follow in other blog posts.


PhD thesis defence

On June 7th Nina Therese Mikkelsen presented her thesis ” Phylogeny and systematics of Caudofoveata (Mollusca, Aplacophora)” for a public audience.  She was questioned by the opponents dr Mikael Thollesson, University of Uppsala, and dr Suzanne Williams, The Natural History Museum of London, and did an excellent performance explaining the results of her studies.

Evolutionary history of cave shrimps

Machumvi Ndogo - preparing for a dive in the dark

Machumvi Ndogo – preparing for a dive in the dark

In 2008 UiB colleagues Kenneth Meland and Endre Willassen surveyed karst caves in Zanzibar together with Hajj M. Hajj in search for aquatic crustacea. Many of these localities have so-called anchialine conditions in which marine water penetrates inland and can mix more or less with fresh ground water.


Atyid shrimps were sampled in salt water about 300 m inland from the coast.

Atyid shrimps were sampled in salt water about 300 m inland from the coast.

One of these sites had three species of small shrimps of the family Atyidae. The phylogenetic relationships of these shrimps have now been analysed by an international team of “cave men” based on full mitochondrial genome sequencing performed at the University of the Balears.

Molecular clock estimates date the relationship of the Zanzibarian species to other known species in the Atlantic and Indo-pacific  to the Cretaceous period.

Shrimps from Osine Cave

Shrimps from Osine Cave

The paper is available from this link:

Species divergence history of the study group.

Species divergence history of the study group. Click for details.

Door # 21: A tale of three fading buck-goats

“Julebukken” – the Yule Goat. 

A goat made of straw has commonly been observed among the paraphernalia that people put on display around Christmas times in the Nordic countries. Ask people what they symbolize and I bet that the majority would say just “Christmas” without having a further explanation at hand. It is very likely that the Yule Goat is a remnant from the pagan celebrations of the December solstice. The mythological origin of the Yule Goat is unclear (see Gunnell 1995).  It is probably of mixed origin because cultural evolution is often syncretic, – a blend of beliefs, mythologies, and practices from different sources and “ethno-folkloristic schools of thought”.  It has been speculated that the straw figure of the Yule Goat reflects some sort of pagan vegetation god ruling over grain growth and who required particular human attention around the winter solstice.

"Julebukk" - a common Christmas decoration.

“Julebukk” – a common Christmas decoration.

Others have associated Yule Goat with the Germanic thunder-god Thor, because he used two bucks to pull his chariot over the sky. Thor must have been an environmentally friendly god because these bucks were used as a food resource in Valhalla and if only he took great care to keep the bones and the skin, he could revive fully reincarnated goats the next day. The idea of a resurrected goat was dramatized in folk rituals of Nordic small communities by people who reenacted the death and revival of the Yule Buck in songs and theater performed on house visits by a ragged assembly of masked people. The central character in these folkloristic plays was a person either wrapped in straw or hides and carrying a goat head, sometimes also a hammer (like Thor). Right up to the mid nineteenth century, plays like these were practiced in Scandinavia. The traditions have several characteristics in common with Halloween and the Yule Buck masquerade apparently is a tradition that now seems to be fading and to be replaced by Halloween celebrations. In both cases there is an underlying theme of temporary breakdown and restoration of cosmological and moral order when cyclic time has gone the full circle. A small scale version of this idea is also at work around midnight, – the ghost hour. The Cristian tradition has tended to associate goats with naughty behaviours of all sorts, particularly in terms of sexuality. Goats were also at times associated with mythological creatures like Pan and with the Devil.

The Star Buck

The Babylonians divided the sky in 360 parts, but ancient astronomers also used twelve 30 degrees sectors of the sky to reference the positions of celestial bodies on the ecliptic, – the track that the sun appears to follow through the year.  Like the classic analogous clock with twelve sectors marking divisions of the day and night the zodiac is a clock for the earth’s revolution around the sun.  Because the rotation axis of the earth is tilted, the sun appears to draw an S-shaped path around the Earth.  From a northern perspective the maximum of the path is the summer solstice. The minimum is the winter solstice, when the zenith of the sun is farthest away from the Arctic and the days are shortest on the Northern hemisphere. The exact time for the solstice is not easy to determine, but ancient astronomers found that the winter solstice took place when the sun was in the sector of the star constellation called Capricornus. Claudius Ptolemy, who is known as the prime authority of  pre-Copernican cosmological texts, wrote in Book 1 chapter 11 of his very influential Tetrabiblos :

“For the sun turns when he is at the beginning of these signs and reverses his latitudinal progress, causing summer in Cancer and winter in Capricorn.”

Capricornus is Latin for “goat horn” and Capricorn is sometimes depicted as a goat, sometimes as half goat, half fish. Because the “turning point” of the sun at winter solstice was once at an imaginary latitude circle drawn through Capricornus, we say that the sun is turning at the Tropic of Capricorn. However, due to the swaying of the Earth’s rotation axis, winter solstice is no longer in Capricorn and the Tropic of Capricorn has also moved away so that, paradoxically, the Tropic of Capricorn is now passing through Sagittarius . When the Julian calendar took effect 45 years BC the solstice was celebrated on 25th of December, but apparently winter solstice was already about to leave Capricornus in the direction of Sagittarius.  Historians of astronomy think that Capricornus was already a marker of seasonal time about 2000 years BC.

The sun in Capricornus seen from Rome 45 years BP according to Stellarium.

The sun in Capricornus seen from Rome 45 years BP according to Stellarium.


The sum at winter solstice in 2016 seen from Rome according to Stellarium.

The sun at winter solstice in 2016 seen from Rome according to Stellarium.

Although much speculation has been put forward about the origins of Yule Buck, I suspect that the role of the goat in the sky has been undervalued when trying to understand the conducts and traditions of people in the Nordic countries around the winter solstice. Surely, the teaching of Ptolemy must have diffused somehow to ordinary people during the Medieval Ages. After all, Capricorn was the messenger of a better existence to come, if one could only sustain over the winter.

Resurrecting a goat
Goats that stood model for the Capricorn have been part of the human environments since long before they were painted on cave walls in Ardeche at the foot of the Pyrenees about 30000 years BC. Archaeological material from Jordan indicates that goats were domesticated already 7000 BC as one of the first of the ruminant species. Wild goats are members of the genus Capra and are distributed with several species over the Eurasian and African continents. Most of the wild goats are now regarded as more or less threatened species due to hunting pressure and habitat loss. In Spain the so-called bucardo goat was declared extinct in year 2000, when the last individual was hit by a falling tree in Oresa National Park.

The extinct subspecies of the Pyrenean Ibex. (Source Wikipedia)

The extinct subspecies of the Pyrenean Ibex. (Source Wikipedia)

An international group of biotechnologists set up experiments to resurrect the bucardo, which is considered as a subspecies of the Pyrenean Ibex, Capra pyrenaica. It is perhaps not likely that these scientists were inspired by the Nordic myth about Thor and his perpetual buck-goats. Nevertheless, they had already taken skin samples from the last living female the year before she died. With the frozen cells from the skin they had cellular nuclei with goat genome and also a plasma membrane with small amounts of cytoplasma. With a technique similar to the one that was pioneered by the Roslin Institute in Edinburgh to clone the sheep Dolly, they replaced the cell contents of domestic goat eggs with somatic cell material from the dead ibex. Then they implanted the manipulated eggs into many substitute mothers of both domesticated goats and of females of the Spanish ibex. Only one of the embryos survived long enough to be released by cesarean section and it died only a few minutes after birth. Despite this and similar failed efforts to reconstruct extinct evolutionary lineages, it is still claimed by scientists who are involved in this business that such methods hold promise for rescuing rare and endangered species. But without making claims of being a specialist in conservation genetics I ask myself: how is it possible to save a species when all of the genetic variability in the population is lost. This may have been a problem already before the population went extinct because the sets of genes that run the immune system and code for the proteins that protect the body from foreign molecules, the so-called major histocompatibility complex, had already been observed to lack variability. Then of course, in the case of the extinct Pyrenean ibex there is also another problem that would be a major impediment in the reconstruction of a natural population. It is a problem of the missing Y-chromosome. Goat Y-chromosomes would be necessary to have functional males of reconstructed goats. Basically this is a problem that has also puzzled thinkers with respect to the child that allegedly was born by a virgin on the solstice 2000 years ago. Did he have a chromosome set from the father?

Merry solstice, Christmas, and Happy New Year!


More reading

Folch, J. et al. (2009) First birth of an animal from an extinct subspecies (Capra pyrenaica pyrenaica) by cloning. Theriogenology 71:1026–1034.

Gunnell, T. (1995) The Origins of Drama in Scandinavia. Boydell & Brewer Ltd.

Hinson, R. (2015) Goat. Reaction Books, London.

Lee, K. (2001) Can cloning save endangered species? Current Biology 11 (7): R245-R246


Door #14: Where the sun doesn’t shine. Lucifer, luciferin and luciferase

Yesterday’s blog was about about Lucia, the mythical virgin who is celebrated with lights produced from combustion energy in candle lights. Lucia’s name is derived from the latin lux, meaning light. Similarly, Lucifer was one who was carrying light. We will not dwell with the ridiculous lore about Lucifer in old folk beliefs. Instead we will briefly look at real carriers of light from the organic world. Light can also be produced with other processes than fire and a range of organisms are particularly skilled in “letting there be light” in their environments. This is what we call bioluminescence. Bioluminescent substance can be used by potential prey animals to scare away predators. (Hover over picture with your mouse to see the gif.)

“Glow worm” beetles or “fire flies” of the families Lampyridae and Phengodidae are familiar to most people who have been out-door on a dark summer night. Studies of fire fly behavior have revealed how different species of these beetles communicate with their kinds using flash signals with variable frequency, intensity and duration. The biochemical mechanisms at work during bioluminescence are also relatively well studied in these beetle groups.

In the marine environments bioluminescence is known from many unrelated organisms and because different molecular reactions are involved in light production it is likely that bioluminescence must have evolved independently many times. A glowing sea may be experienced when massive densities of dinoflagellates are flashing their lights on the coast at night. Particularly Noctiluca scintillans, whose body is big enough to be visible with the naked eye, is frequently referred to in field guides to marine shore life. But many dinoflagellate species are involved in the bioluminescence that Norwegians call “morild”, – the “fire in the sea”. This phenomenon has also been called phosphorescence, however this is the process where light energy is absorbed by a substance and emitted on a different wave length. Special fluorescent proteins are responsible for glow-stick effects in organisms. (Incidentally the Greek light-carrier Phosphorus has been equated with the Latin Lucifer, and those of us who have seen white phosphorous in action understand what gave the name to this very reactive version of the element.) Studies of dinoflagellates have associated the light production with molecular bodies named scintillons and demonstrated that the biochemical activity in these objects in diatoms is governed by diurnal rhythms. This appears to make sense, because what is the point of flashing lights at day time? It may not be quite clear what use the diatoms have of producing light at night time either. However, it seems more obvious that there are functional advantages of bioluminescence in the depth of the ocean, where light does not penetrate. And it is below the so-called euphotic zone, from approximately 200 m on that bioluminescence is effective in different sorts of interactions among various animal groups. Deep water angler fish even use lit lures to attract prey.

Light emission in some animals is based on symbiosis with bacteria such as Aliivibrio fischeri.  In other cases, the animal itself may produce the active proteins. Different biochemical systems are at work in bioluminescence and the light-producing molecules are not the same in all systems. Still, as a group of oxidizing and light emitting molecules they all go by the name of luciferin.  To produce a light flash a catalyzing agent is also needed. This is provided by a group of different enzymes called luciferase.  Other active components and free ions may be involved in the reaction which may be triggered in different ways, either mechanically as with a set of oars and a rowboat when dinoflagellates are near the surface water, or by some biochemical trigger. Sometimes it must happen by some neural response in the animal.

Light organs in the lantern fish Benthosema glaciale. (from Paulsen et al. 2013

Light organs in the lantern fish Benthosema glaciale. (from Paulsen et al. 2013)

The lantern fishes are known for their photophores, – series of small organs that can produce yellow, green or blue light. Because the arrangement of photophores is different in different species, the organs are thought to play a role in communication between con-specific individuals. This may be the case for other animals as well, such as squids. It is also believed that the light organs can have a camouflaging effect by visually breaking up the silhouette of the fish, when the fish is viewed against a lighter back-ground higher up in the water column. The fish thus obtains protection from predators below by means of counter-illumination.

Several deep water animals are confusing potential predators by ejecting a luminescent substance towards the predator. Shrimps of the family Oplophoridae are particularly known to exercise this defensive technique.  The luciferine in shrimps is called coelenterazine and is presumably produced in the digestive gland called haepatopancreas. When the shrimp spews the glow through the mouth, the effect is somewhat similar to the one that cephalopods use when they disappear in a cloud of ink.  May we call it a “lucifer smoke-screen”?

Our museum collections have a rich material of these shrimps. Several species were collected during the MAR-ECO cruises over the Mid-Atlantic Ridge. One of them was Oplophorus spinosus shown in the picture below. While all of the oplophorids appear to be able to use a “lucifer smoke”, some of the species, including O. spinosus, also have light producing organs along their sides, somewhat similar to what we see in the lantern fishes. These photophores are complicated light generating organs with lenses and reflectors. They may be able to filter the wave length, and also the intensity and direction of the emitted light. In oplophorids, such organs are only found in three of the most closely related genera of the family, according to a recent study by Wong et al. (2015).  Interestingly, these animals also have two types of eye pigments. One type is shared with other oplophorids and is sensitive to the blue-green part of the light specter.  The other pigment is also sensitive to the shorter wave length in UV light. Because of the special abilities of the eyes it is tempting to think that these shrimps somehow are using the photophores in communication with individuals of their species. If so, Oplophorus spinosus and similar light talk would be a perfect case for biosemiotics. “Please shrimp, tell us about the world view from your perspective!” However, it is possible that the use of the photophores is only for counter-illumination when the shrimps are performing vertical migrations in the water column.

Oplophorus spinosus - a bioluminescent mid water shrimp (Photo: David Shale, MAR-ECO)

Oplophorus spinosus – a bioluminescent mid-water shrimp carrying large eggs (Photo: David Shale, MAR-ECO).

The “signalling abilities” of bioluminescent compounds are exploited in biotechnology and cell research. Luciferase from Oplophorus has been exploited as a so-called reporter gene in visualization of cell activities and gene transcription. May be it is not too far-fetched to see the shrimps as some kind of “light-carriers”.



Inoue S, Kakoi H, Goto T. (1976) Oplophorus luciferin, Bioluminescent substance of the Decapod shrimps, Oplophorus spinosus and Heterocarpus laevigatus. J.C.S. Chem. Comm. 966:1056-1057.

Poulsen JY, Byrkjedal I, Willassen E, Rees DJ, Takeshima H, Satoh TP, Shinohara G, Nishida M, Miya M. (2013).Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of Myctophiformes (Neoteleostei). BMC Evolutionary Biology 13:111.

Shimomura O, Masugi T, Johnson FH, Hanedal Y. (1978) Properties and reaction mechanism of the bioluminescence system of the deep-sea shrimp Oplophorus gracilorostris. Biochemistry 17:994-998.

Wong JM, Pérez-Moreno JL, Chan T.-Y, Frank TM, Bracken-Grissom HD. (2015) Phylogenetic and transcriptomic analyses reveal the evolution of bioluminescence and light detection in marine deep-sea shrimps of the family Oplophoridae (Crustacea: Decapoda). Molecular Phylogenetics and Evolution 83:278–292

Door #13: Lucia – with a ray of enlightenment?

Many kids will appear as “lucifers” today – light bearers. Celebration of Santa Lucia’s day seems to have won increasing popularity in Norway over the recent decades. Much of this cultural practice has clearly spread from Sweden, where the tradition is so deeply rooted since early 1900 that Swedish racists seem to believe that Lucia was an Arian blonde from remote mythical times of Astrid Lindgren’s Småland? But according to legend, Lucia was a christian martyr from Sicily in the fourth century. The story goes that she was tortured because of her conviction. She obtained her post mortem status as a heroine because she sacrificed her eyes for the “true faith” and was thus expelled to the darkness.

"Lussekatt" is a pastry made for Santa Lucia day. Is it supposed to express the track of the sun through the year?

“Lussekatt” is a pastry made for Santa Lucia day. Is it supposed to express the track of the sun through the year?

Norwegian Wikipedia (of “Luciadagen”) claims that Lucia day has no actual association with Advent. “It is simply a celebration in commemoration of Sta. Lucia’s death on the 13th of December”, it is stated. But wait a minute! Take some time to look at the two calendars from the year 1700 that I reconstructed with the Timeanddate facility. This was the year when the Gregorian calendar revision was finally introduced in Denmark-Norway. Until that time Scandinavians had used the calendar that Julian Caesar’s government introduced 45 BC.

Reconstructed calendars for Denmark-Norway and Sweden from the year 1700. Notice that Norwegian Christmas Eve and Swedish Santa Lucia day are on the same day,

Reconstructed calendars for Denmark-Norway and Sweden from the year 1700. Notice that Norwegian Christmas Eve and Swedish Santa Lucia day are on the same day,

The Julian calendar is assuming a mean year length of 365.25 days, so the Julian clock was ticking about 20 minutes too fast compared to the mean tropical year. The Earth moves around the sun with a speed of about 30 km per second. As observed from the Earth, the mean time it takes for the Sun to return to the same point in the annual revolution is the tropical year. Revolution time is slightly variable, but since it is closer to 365.24 than to 365.25 the mismatch between the calendar and the season was increasing one day about every 128 years. In order to correct for the 10 days accumulated difference, the new Gregorian calendar was introduced in the catholic world in 1582.

Protestant Scandinavian countries may not have been able to discriminate between science and catholic religious practices. They delayed any action with the calendar until 1700 when the seasonal anomaly had increased to 11 days. In Denmark-Norway it was decided to delete those 11 days from the last part of February so that March 1st would follow immediately after February 18. The Swedes decided to go for a more gradual procedure. They reckoned that the calendar would be in order with time if they just neglected some successive leap years and skipped February 29 for some time. So they took this first small step by deleting February 29 in 1700. You can see how that worked out for February in the two calendars.

Travelling across the Norwegian-Swedish border in 1700 would imply the crossing of “multiple date lines”. Although it is questionable whether Lucia was celebrated to any extent in Sweden at the time, we could imagine that we wanted to travel there to take part in the feast for this catholic saint on the 13th of December. The Swedish calendar would show that Lucia is the fourth day in week number 50, which was a Thursday. However, the fourth day of week 50 in Norway was the 23rd. If we remember that the adjustment to the Gregorian calendar in 1700 should imply deletion of 11 days and that Sweden only got rid of one of those, we should rather consider the fifth day of week 50, namely Friday the 24th as the one that compares to Lucia day in Sweden. So with a couple of not particularly magic calculations we have matched Lucia’s deathday with Christmas Eve!
Could it be that these two mythical celebrations are actually rooted in fancy human imagination spun around the same astronomical event? Certainly so because in the course of time the Julian date for the winter solstice changed from 23rd to 22nd in the first centuries and in the 13th century the happening was down to 13th of December. This is the simple explanation to why some are confused by the fact that Lucia’s day is also called the darkest day of the year. Well, dear Swedes and sweet-hearts. Not any more.
We know that winter solstice, the day when the track of the sun has reached its southernmost point at the moving Tropic of Capricorn, was measured already 5000 years ago by stone age people at Newgrange in Ireland. During the regime of Julius Caesar the winter solstice was dated by Roman astronomers to December 25th and this became the celebration of the sun god Sol Invictus in the Roman Empire. However, the list of solar deities in pre-Cristian cultures is a long one and celebrations of winter solstice were significant in many pagan traditions before the customs were absorbed by Christian ways. Various brands of mystics still seem to recognize winter solstice as a moment of great spiritual significance. But maybe it would be sobering to think of the phenomenon in terms of solar energy influx and the amazing cascading biological effects of the seasons. In biology is where the mysteries are. Indeed the solstice marks an ecological and existential turning point for life on the northern hemisphere. At times it was dated to the 13th of December. This year it is happening on December 21st at 11:44.


And we teach

In the practice part of the regular UiB Phylogenetics course (BIO332) we also invite participants from other Nordic universities who are members or associates of ForBio, the Research School in Biosystematics. This time we had guests from the University of Iceland, the University of Tromsø, the University of Nordland, the Norwegian University of Science and Technology, the University of Oslo, Uppsala University, and University of Copenhagen.

Computer practice with tools for phylogenetic analysis. UiB 2015

Computer practice with tools for phylogenetic analysis. UiB 2015