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 BOLDSYSTEMS.org.
Having submitted your query to BOLD, you wait for some seconds for results. In this example BOLD returned the following window.
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.
The species page for Atelecyclus rotundatus gives us more information about this crab and about its records in BOLD.
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.
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.
Click your way over and read about the Deep-sea lyre sponge – Chondrocladia lyra, the Palauan primitive cave eel – Protanguilla palau, the Deep-sea acochlidiacean slug – Bathyhedyle boucheti, the Tree syllid worm – Ramisyllis multicaudata, the Starry sea wanderer jelly – Marivagia stellata, the The Hoff crab – Kiwa tyleri, the Squidworm – Teuthidodrilus samae, the Jesse Ausubel’s ‘terrible claw’ lobster – Dinochelus ausubeli, the ‘living fossil’ octocoral – Nanipora kamurai, and the Scaly-foot snail – Chrysomallon squamiferum.
“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.
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.
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.
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!
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
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.
We’re currently busy with a workshop on Marine Invertebrates of West Africa , look here for news on that:
On the 27th January we left the subtropical latitudes and moved into the tropics where we established our base-camp in the town of Vilanculos overlooking the Bazaruto Archipelago Natural Park – a string of six islands surrounded by coral reefs. Regrettably a spiral of bureaucracy and administrative complications made impossible to obtain the necessary collecting permit to sample in the pristine reefs of the Natural Park. Alternative good sampling sites were not that easy to find and the weather conditions also didn’t help much with strong winds and some rain, resulting in a very choppy sea. We decided to move back south one day before scheduled and spend two days in the village of Paindane with great tidal and inshore reefs housing an extraordinary diversity of slugs. Here we sampled both at night- and day-time and was impressive to see the faunal differences between these two periods of the day.
On the 2nd February we travelled back to the village of Zavora where we had meet for the beginning of the campaign. We spend the last three days sampling in Zavora a truly hot spot for marine slugs; the diversity in the tidal and subtidal reefs exceeds anything I have experienced before. My colleagues from the Zavora Marine Lab have already registered the occurrence of nearly 200 species in these reefs and even so we managed to add to the list a few more!
Overall, about 80 species were collected during our fieldtrip but the identification of several of them requires now detailed study and will integrate ongoing projects at the Natural History Museum of Bergen.
The tropical Indo-West Pacific harbours the highest diversity of marine life in the World with many species still undescribed. In the region, the eastern coast of Africa is one of the less studied areas and few opisthobranchs gastropods have been recorded in Mozambique with a coastline of 2,700 km stretching across sub-tropical and tropical latitudes.
Together with colleagues from the Zavora Marine Lab (Mozambique) I will be surveying the southern part of Mozambique between the village of Zavora – approximately 500 km north of the border with South Africa – and the tropical archipelago of Bazaruto. This 3-weeks fieldtrip (16 Jan–6 Feb) is part of an effort to document the diversity of opisthobranchs at a global scale and to understand the biogeography and speciation patterns of these molluscs.
After a couple of initial days in Zavora we headed north to the region of Inhambane, famous for its aggregations of manta rays and whale sharks where we spent about a week sampling for the far most spectacular sea slugs!
Barcode Bulletin is a newsletter from International Barcode of Life (IBOL). Barcode Bulletin Vol. 4, No. 2 – December 2013 has recently published two stories about activites we are involved in. One nice piece of news is that the Norwegian Biodiversity Information Center and the Research Council of Norway has decided to fund the NorBol consortium. The other news are about our summer 2013 workshop in the MIWA-project which was co-funded via IPBES.