In this project we will sample a few hundreds of individuals per species, regularly distributed over the study area that likely contains the imprint of several microrefugia. After DNA extraction, each sample will be sequenced on an Illumina sequencer (HiSeq) using a shotgun approach, with the goal of obtaining at least six million sequence reads. This approach has been called “genome skimming”. It will allow us to assemble the whole chloroplast genome, the great majority of the mitochondrial genome, and the nuclear ribosomal tandem repeats.
What will the genetic data bring?
A spatial analysis of the variants of the mitochondrial and chloroplast genomes and of the nuclear ribosomal DNA should allow us to identify the individuals originating from the same microrefugium. We expect that individuals originating from the same microrefugium have the same variants of mitochondrial DNA and are geographically grouped. For instance, for Cedrus, the geographic distribution of the chloroplast DNA variants should also provide information on the importance of male mediated gene flow.