Résumé
The comparative study of patterns of genetic diversity in crops and their wild ancestors coupled with recent advance in coalescent theory opens the way for making some historical inference on the demographic (and possibly selective) processes that have shaped genetic diversity in crops since domestication. Demographic events affect genome-wide levels of polymorphisms and the spectrum of allelic frequencies. Some forms of selection, in particular recent selective sweeps are expected to reduce diversity locally that is at the target of selection and in surrounding areas in the genome. Although a full reconstruction of the demographic history seems impossible based on patterns of polymorphism alone, contemporary polymorphism data can be used to calibrate simplified demographic models that can account for amounts and patterns of currently observable diversity. We illustrate that approach in two crop species with contrasted histories and mating systems. First, patterns of diversity are studied in the (allo)tetraploid wheat (Triticum turgidum) complex a species with a mixed mating system dominated by high levels of selfing. The intensity of bottlenecks associated with major historical episodes of domestication and subsequent selection are quantified using microsatellite markers. Patterns of microsatellite diversity are also compared with patterns of sequence polymorphism detected at the Gsp-1 locus. We find that domestication and subsequent selection resulted in a massive loss of genetic diversity and estimated a several fold reduction in the long term effective size realized in cultivated wheats relative to their wild ancestors (even after accounting for the probable loss of diversity in wild populations due to extensive habitat loss since Neolithic times). Next we analyze patterns of nucleotide diversity in alfalfa (Medicago sativa) an autotetraploid and outcrossing crop species. Sequence polymorphism among individuals spanning a wide geographic distribution was surveyed and analyzed at two intronic regions. These were located in respectively the alfalfa NADHdependent glutamate synthase and PO146, a pollen pectate lyase-like gene. These genes were chosen while searching in GenBank a public genetic sequence database for nucleotidic sequences of M. sativa and not chosen with any phenotypic à priori. This allowed us to i) quantify the extent of genetic divergence between wild and cultivated populations and thereby assess the impact of domestication on this divergence, ii) assess the originality of the genetic makeup of wild Spanish populations of alfalfa relative to the rest of extant population throughout the species range, iii) determine whether there is likely ongoing (recent) gene-flow among wild and cultivated populations in Spain