The Chamois Genome Project
|Director of thesis||Alexandre Reymond|
|Co-director of thesis||Marc Robinson-Rechavi|
|Summary of thesis||
A lot of scientific studies have been performed involving nature and close to nature. This time again, we get into the nature and the wild life and aim to study the phylogeography of chamois (Rupicapra rupicapra), an emblematic species of the Alps.
The chamois are useful species to investigate the combined genetic impact of habitat fragmentation, over translocation. The chamois are one of the most common animals found in the European mountains. The current taxonomist believes that, two species of chamois exists and they were categorised on the basis of morphological and behavioural characters. Rupicapra rupicapra assembles the northeastern populations of the Alps along with the Jura (R .r. rupicapra), the Chartreuse (cartusiana), Balkans (balcanica), Tatras (tatrica), Carpathian (carpatica), Caucasus (caucasica) and Pontic mountains (asiatica), while R. pyrenaica groups the populations from the Pyrenees (R. p. pyrenaica), the Cantabrian (R. p. parva) and the Apennine mountains (R. p. ornata).
Till date there is a controversy about the taxonomy of the Chamois. Some researchers suggest that R. p.ornata should be promoted to species rank, while others suggest that only one species should be considered for all the chamois populations.
Recent studies by Lovari et al. provide evidence to the limited analyses with molecular methods targeting allozymes, mitochondrial and nuclear DNA. Hence, the studies ended up giving conflicting results and failed to determine the mono or polyphyly of Rupicapra, or the existence of the number of species and subspecies.
Therefore, we aim to determine the population structure of the Alpine chamois (Rupicapra rupicapra), as well as resolve the controversy about the taxonomy of the Rupicaprinae. Furthermore, if the species and subspecies occur, then at what point the speciation occurred is also another question, which we aim to resolve.
In order to give life to this project and drawing a concrete conclusion to the ongoing controversy, the genome of the chamois has recently being sequenced. A pair of 100bp sequences separated by 500-5000bp of genomic space using specifically engineered libraries allowing genome assembly was generated. Therefore, a scaffold of the chamois genome has been created. Since two different individuals have been sequenced, a comparative analysis can be performed between the two large datasets obtained and analysis of data on the large set of polymorphisms could assess the variation and potentially identify the hierarchy that corresponds with geographic and the ecological differences among population. Therefore, leading to a better understanding of the phylogeography of the Rupicaprinae species and finally resolve the population structures and the eventual admixing.
Furthermore, multiple tissues such as, heart, liver, muscle, lung, spleen, kidney, bladder has also been collected in order to generate the transcriptome data by RNA-seq. Proper analysis of the datasets can also give a different dimension to the research and help in resolving the controversy.
This project is at its initial stage right now. However, we believe to progress well with time and resolve the questions that the world has raised regarding the phylogeography of the Rupicaprinae.
|Administrative delay for the defence||20.11.2017|