The identification of cultivated plant centers of origin is of growing interest since the pioneering work of Nikolaï Vavilov. Cultivated species generally show a high level of genetic diversity in their center of origin, thus identifying these areas would have important implications for the conservation and sustainable management of their genetic resources. We aim to identify the center of origin and to infer recent evolutionary history of one of the most emblematic spice tree species ¬¬– nutmeg (Myristica fragrans; Myristicaceae). The species is thought to originate from the Banda islands (Southern Moluccas archipelago, Indonesia), but this has never been confirmed. We characterized the genetic diversity of this species across the Moluccas archipelago using recently developed nuclear microsatellites markers and whole plastid genome sequences. We found two main intra-specific genetic clusters: one in South Moluccas (Banda and Ambon islands) and another in North Moluccas (Ternate, Tidore and Bacan islands). The latter cluster showed higher genetic diversity than the South Moluccas cluster. We then inferred the demographic history of nutmeg and evaluated different evolutionary scenarios using Approximate Bayesian Computation (ABC) analyses. Populations from South Moluccas show patterns of a recent bottleneck, whereas North Molucca populations did not. Moreover, South Moluccas populations are inferred as ancestral, with subsequent population migration to the North Moluccas during the late Pleistocene to early Holocene period. These results have strong implications for conservation strategies of nutmeg.

Analysis of the genetic bases of adaptation to climate changes are often conducted on natural populations. We report here on a study based on diachronic sampling (1980 & 2010) of the self-fertilising crop species, Oryza sativa (Asian rice) and Oryza glaberrima (African rice), in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+1°C on average) and rainfall regime (less predictable and reduced amount) in the target area. Second, phenotyping the populations for phenology, we observed significantly earlier heading time (up to 10 days) in the 2010 samples. Third, we implemented two genome-scan methods, one of which specially developed for selfing species, and detected 31 independent selection footprints. These loci showed significant enrichment in genes involved in reproductive processes and bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. We argue that this high adaptive potential results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds well before the advent of the environmental selective pressure. The complex selection footprints observed in this empirical study calls for further model development on genetic bases of plant adaptation to environmental changes.