Retracing the centre of origin and evolutionary history of nutmeg <i>Myristica fragrans</i> , an emblematic spice tree species

Identifying the centres of origin of cultivated plants is important for conservation and sustainable management, since this is where these species tend to be most genetically diverse. This research seeks to determine the centre of origin and evolutionary history of nutmeg (Myristica fragrans; Myristicaceae), an emblematic spice tree species traditionally believed to originate from the Banda Islands, South Moluccas, Indonesia. We explored nutmeg's genetic diversity and structure across the Moluccas archipelago using nuclear microsatellite markers and whole plastid genome sequences. Two primary intra-specific genetic clusters were found: one in the North Moluccas (Ternate, Tidore and Bacan islands) with higher genetic diversity and another in the South Moluccas (Banda and Ambon islands), which exhibited signs of a recent bottleneck. Although the North Moluccas showed higher genetic diversity, approximate Bayesian computation analyses supported South Moluccas as the centre of origin of M. fragrans. The species migrated from South to North Moluccas during the late Pleistocene to early Holocene period and experienced a recent bottleneck in the South. These findings suggest a naturally driven distribution influenced by migration and past climate changes. Human activities have further shaped these patterns, offering insights for developing targeted conservation strategies for nutmeg based on its genetic diversity.