Skip to main content
Dryad

Retracing the center of origin and evolutionary history of nutmeg Myristica fragrans, an emblematic spice tree species

Kusuma, Jakty1; Couderc, Marie2; de Navascués, Miguel3; Gérard, Pierre R.4; Scarcelli, Nora2; Duminil, Jérôme2

Published Feb 04, 2026 on Dryad. https://doi.org/10.5061/dryad.qjq2bvqm0

Data files

Feb 04, 2026 version files 18.97 MB

Click names to download individual files

Abstract

The study of plant origins, since Nikolaï Vavilov's foundational work, emphasizes the importance of identifying centers of origin for cultivated species, which exhibit high genetic diversity in their native areas, impacting conservation and sustainable management. This research seeks to determine the origin and evolutionary history of nutmeg (Myristica fragrans; Myristicaceae), traditionally believed to originate from Indonesia's Banda Islands in the Southern Moluccas. We explored nutmeg's genetic diversity across the Moluccas archipelago using nuclear microsatellite markers and whole plastid genome sequences. Our results identified two primary genetic clusters: one in the North Moluccas (Ternate, Tidore, and Bacan islands) with higher diversity, and another in the South Moluccas (Banda and Ambon islands), which exhibited signs of a recent bottleneck. Through Approximate Bayesian Computation (ABC) analyses, we inferred that nutmeg migrated from South to North Moluccas during the late Pleistocene to early Holocene, confirming the South Moluccas as its center of origin. These findings suggest a naturally-driven distribution influenced by migration and past climate changes. Human activities have further shaped these patterns, providing essential insights for developing targeted conservation strategies for nutmeg based on its genetic diversity.