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.