Investigation in the depths of nature

The night of the pangolin
Febbraio 7, 2017
Through the forest
Febbraio 9, 2017

Twenty-four is the number of species that Minion can analyze simultaneously. Hundreds of thousands of sequences go through the protein-based microchannels of the thin layer of nanopores of the Minion flowcell, deciphered by the device according to the letter sequence characteristic of every species. This time Anita has prepared 6 different DNA samples belonging to reptiles, amphibians and mammals. This DNA, once extracted, purified and amplified, will reveal the identity of another 6 inhabitants of the Kabobo forests.

One of the samples is from the famous pangolin skin received a few days ago. The others come from a Cephalophus, a small forest antelope, a Xenopus and a Leptopelis, two amphibians, a snake of the Lycophidion variety and a lizard of the Trachylepis type. The comparison between the obtained sequence and the ones present in the GenBank will allow us to define the genetic divergence with the most similar species published to date.

“We downloaded from the database all the data belonging to the Concordati group. This allows us to carry out the comparison (technically called blast) offline, that is, without needing to have an internet connection.  Massimo sits at his computer to verify the outcome of the blast, “What do you expect to find?”, I ask Anita, “ First of all a confirmation that the treatment of the DNA has been effective, by which I mean that it hasn’t been tainted by our skin fragments or saliva, and that we haven’t contaminated the samples with each other. If the comparison confirms that the pangolin is indeed a pangolin, and the antelope is an antelope, it will mean that it has all gone to plan and the two animals’ DNA are pure.

Okay, it is the moment we have been waiting for. Massimo presents the results: in the case of the Trachylepis maculilabris lizard and the Xenopus victorianus amphibian, the sequencing shows us 99% similarities. Anita rejoices. It’s all gone well, the species have been confirmed. The tree pangolin shows a 97% similarity, leaving a 3% difference with the GenBank’s documented species. This result appears to confirm the level of isolation in these forests, just as the 4% divergence of the Leptopelis type does. In regard to the antelope’s blast, or rather the comparison of our sequence with those in the data bank, we find an analogy of 96% with the Cephalopus Callipygus, a species widespread only in western Africa, in an area 2000km away from our location.

“The sister species”, Michele explains, “is the C. Weynsi, whose sequence is not present in the GenBank. The correspondence with other local species (C. nigrifrons, C. silvicultor e C. dorsalis, C. leucogaster) is lower, between 94 and 95%. This excludes the possibility of our sample belonging to one of these species. Further research is necessary to understand if the antelope to which the sample belongs is a C. Weynsi or another. These first results, which will need to be confirmed with further analysis, are the first concrete contribution of the Kabobo Expedition to establishing a new National Park in this area.

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