Data from: Evolutionary history of almond tree domestication in the Mediterranean basin

Genetic diversity of contemporary domesticated species is shaped by both natural and human-driven processes. However, until now, little is known about how domestication has imprinted the variation of fruit tree species. In this study, we reconstruct the recent evolutionary history of the domesticated almond tree, Prunus dulcis, around the Mediterranean Basin, using a combination of nuclear and chloroplast microsatellites (i.e. SSRs) to investigate patterns of genetic diversity. Whereas conservative chloroplast SSRs show a widespread haplotype and rare locally distributed variants, nuclear SSRs show a pattern of isolation by distance with clines of diversity from the East to the West of the Mediterranean basin, while Bayesian genetic clustering reveals a substantial longitudinal genetic structure. Both kinds of markers thus support a single domestication event, in the eastern side of Mediterranean basin. In addition, model-based estimation of the timing of genetic divergence among those clusters is estimated sometime during the late Holocene, a result that is compatible with human-mediated dispersal of almonds out of its center of origin. Still, the detection of region-specific alleles suggests that gene flow from relictual wild pre-glacial populations (in North Africa) or from wild counterparts (in the Near-East) could account for a fraction of the diversity observed.