INTRODUCTION
Inferring the center of domestication of a cultivated species is challenging. The development of agriculture occurred independently in different parts of the world from 11,000 to 5,000 years ago. Alphonse de Candolle was one of the first to question the geographical origin of cultivated plants using an integrated scientific approach . He synthesized data from different disciplines (botany, plant biogeography, archaeology, paleontology, history, linguistics, ethnology) to propose hypotheses about the geographic origin of 247 cultivated species. This work was later extended by Nikolaï Vavilov, who proposed main centers of domestication for cultivated plants . Vavilov’s work has since been revisted and updated by others . Indeed, the centers of plant domestication sensu Vavilov was subsequently confirmed by a number of archaeological findings . Furthermore, additional progress has been made on this topic through the use of genomic data to study the origin of cultivated plants . However, despite these recent progress in research, the origins of many cultivated species still remain poorly understood.
Inferring the place of origin and biogeographic history of a cultivated species is important to develop robust conservation and sustainable management strategies. Generally, the genetic diversity within a species is not homogeneous across its distribution range. The center of origin of cultivated plants typically presents higher levels of genetic diversity than their introduced populations as species propagation practices outside of its original distribution range often results in genetic bottlenecks . Identifying the center of origin of a target species is thus of utmost importance to develop conservation strategies that ensure the safeguarding of potentially valuable genetic resources. However, it is worth noting that this expectation can be obscured by gene flow with closely-related species, a relatively frequent phenomenon in plants . Indeed, during their propagation outside of their native range, cultivated species may enter into contact with closely-related species, creating new possibilities for interbreeding and increase of genetic diversity in the domesticated pool. This process is known to contribute to species adaptation to new environmental conditions during its propagation outside of its native range .
Genetic studies based on extensive sampling across a species’ distribution can contribute to tracing back the biogeographical history of that species . For non-model organisms with a few genomic resources available, two types of genetic markers are commonly used: nuclear microsatellites (nSSR) and chloroplast DNA (cpDNA). These markers are used to infer past demographic events and to test different demographic scenarios with temporal calibrations .
Nutmeg, Myristica fragrans , is one of the most emblematic spice tree species. The exact location of the center of origin of the species is controversial, some authors hypothesize it to comprise a whole archipelago in Indonesia, the Moluccas (Maluku in Indonesian, also known as ‘the Spice Islands’), whereas others mentioned the Banda islands only–a group of small islands in South Moluccas (Figure 1). The trading history of spice species has fascinated many, as evident in the extensive literature found on this topic. The Chinese were among the first involved in the trading of these species, with the earliest description of Banda islands and the nutmeg in the XIVth century . A short entry from Zhao Rugua’s diary (c. 1225) seems to be the earliest written mention of the nutmeg. Unfortunately, the vocabulary used in this old text was insufficient for a definite identification of the species and region involved . The Portuguese were the first European explorers arriving in the region in search of the Spice Islands in the 16th century. They cite Banda islands as the center of production of nutmeg, suggesting that the cultivation of this species mainly took place on these islands during that time. Yet, Rumphius in his Herbarii Amboinensisexplained nutmeg is distributed throughout the entire Moluccas: “The Nutmeg Tree is much further distributed than the Clove tree, to wit, throughout almost the entire Moluccas, though its true see is the Province of Banda , …” (though ‘its true see’ is in Banda archipelago ( English translation by E.M. Beekman of the latin original text ‘verus tamen ejus locas fixus est Banda’)⁠. The words of Rumphius are not necessarily easy to interpret, and we might understand either that the native range of the species is the Banda archipelago (which has been repeatedly cited as such thereafter) or, that Banda islands represent the place where the species was cultivated at that time.
What is known with certainty is that Banda islands were the most important places of nutmeg cultivation during the Indonesian Dutch period (ca. 1600-1800). At this time, the Dutch East India Company (Vereenigde Oostindische Compagnie, VOC) applied a strong monopolistic policy to ensure its control over this important economic resource . Other European nations, such as France or England, did their best to circumvent the Dutch monopoly by getting planting material from Banda islands to propagate the tree in their tropical colonies . This part of history probably strengthened the general view that nutmeg’s place of origin was Banda islands. Nowadays, the species is widely cultivated in different places in Indonesia and other tropical regions of the world.
Few archaeobotanical studies were conducted in Indonesia. To the best of our knowledge, only one study has identified historical traces of nutmeg consumption in Indonesia before European arrival . This study was held in one of the Banda islands, Pulau Ay (in English known as Ai Island), and traced the consumption to the Neolithic period (ca. 3500–2000 B.P.). Traces of consumption do not necessarily imply that nutmeg was cultivated at that time, but nevertheless this piece of evidence indicates the presence of the species in the Banda islands since more than 1000 years ago.
To address this gap in knowledge on the ancestral distribution of nutmeg, we applied a population genetic approach to improve our understanding of the biogeographical history of nutmeg in the Moluccas. More specifically, we tested whether the species originated from the Banda islands, or from the wider Moluccas. We sampled the species across several Moluccas islands from North to South, and characterized its genetic diversity using a set of recently developed nSSR and whole plastid genomes.