The frog’s identity

The Kabobo party – The Congolese soul of the Kabobo Expedition
Febbraio 11, 2017
Febbraio 14, 2017

The frog’s identity

It’s half past ten in the evening when finally, after 15 hours of uninterrupted work, Anita turns off her headlamp. She has just completed the last  step of the seemingly endless protocol required for the first sequencing of the Kabobo Expedition. But the work has not yet ended. In order to know if her work has been successful we have to wait another 20 minutes in which Massimo, with the help of equipment no larger than an external disc, will proceed with the actual sequencing needed to distinguish the DNA of one species from another. The first strand of DNA to be examined is taken from a frog found in a stream not far from the camp. A phalanx is sufficient  to obtain the information Massimo and Anita are looking for. The DNA has been extracted, purified and amplified in one day of intense work, carried out under the imposing mango tree facing the Tanganica lake where yesterday we equipped the field laboratory. The process seems never ending, and even though Anita cheerfully says that a laboratory protocol “is a bit like a recipe” it is clear that she is really tired.

The biological description of Kabobo, our objective in this expedition, plays an important role for its protection. The knowledge of the mountain’s biodiversity will add value and weight to the bid to make it a protected area. Not to mention if we were to discover a new species, with every probability of it being widespread on the mountain. For these reasons Massimo and Anita’s presence here, in one of the most remote areas of the planet, is of revolutionary significance. Here they work nearly submerged in hundreds of phials, pipettes, centrifuges and various futuristic technologies. Up till now, after field research, and a complex procedure to extract tissue for genetic analysis, there has been a long phase of exertion, patience, expense and time: the tissue needed to be exported from the town of its extraction, transported to a laboratory where it would get analyzed (after remaining on a waiting list for some time) with expensive equipment.

Two years ago the same team had, for the first time, tested the field technology in a Tanzanian forest. Thanks to an online connection the first sequence was then sent to Italy. This time, however, we took a step further. The current expedition aims to complete the sequencing procedure completely offline and to put it to the test with different animals, such as reptiles, amphibians and mammals, including the Pangolin’s skin offered to Anita a few days ago.

Anxiously we stare at Massimo’s computer screen, to which Minion is connected, a nanopore device developed by Oxford Nanopore Technologies that is able to sequence in a few minutes hundreds of thousands of DNA traits. If the software works, the 15 hours of Anita’s hard work will result in the name of the first species of the Kabobo Expedition.

The software starts! We rejoice, Anita is moved. When all the DNA fragments have been deciphered, a process called blasting will allow us to compare the results with those in the GeneBank, the vast gene bank that contains all the genetic sequences so far shared. The comparison will make it possible to identify a species or to determine, in the event the sequence found has no similar enough match, if the species we have come across is unknown.

The results? 96% similarity with the Amietia delalandi’s DNA. This means that our sequence has a 4% difference to the bank’s closest sequence, the delalandi. From a genetic point of view, to be able to identify a species with positivity, the difference has to be within 2%. This means either our frog is a very different delalandi, in which case it would confirm the evolutionary uniqueness of Kabobo, or it is an entirely new species. A great start to our expedition!

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