Drastic environmental changes, such as the climatic oscillations of the Pleistocene, have dramatically influenced the level and spatial organization of species genetic diversity. In Europe, the impact of such environmental alterations on the genetic structure of long-lived plant species is well documented, but little information is available for annual. Therefore, this thesis aimed to establish large scale phylogeographies for annual species, and we focused on the two widespread European species of the annual genus Rhinanthus (Orobanchaceae): R. angustifolius and R. minor. Genetic variation was investigated using of chloroplast DNA (cpDNA) sequences and amplified fragment length polymorphisms (AFLPs) in both species. For R. angustifolius, genetic variation revealed by AFLPs was clearly structured geographically, and yielded various phylogeographic hypotheses similar to what is generally observed for long-lived species. Contrary to AFLPs, the cpDNA variation observed did not show any clear geographic structuring. To explain such incongruities between the patterns revealed by cpDNA and AFLPs, wide-ranging hybridization with the closely related R. minor has been proposed. Confirmation of the importance of hybridization between these species came from the investigation of genetic variation within and among R. minor populations, which revealed an extensive and geographically structured cpDNA haplotype sharing. At the same time, the congruent cpDNA and AFLP patterns found in R. minor indicated that hybridization did not affect the phylogeographic survey of this species and confirmed observation of a local asymmetric introgression toward R. angustifolius. Furthermore, related to these phylogeographic investigations, experimental crossing confirmed the general rule of matrilineal inheritance of the chloroplast genome in Rhinanthus, and preliminaries investigations of the relationship between genetic and morphological variation were conducted.
Vrancken, J. (2010). Individual and comparative phylogeography of Rhinanthus angustifolius and Rhinanthus minor in Europe. https://hdl.handle.net/2078.5/99208