at nSSR loci
We found a total number of 210 alleles using the 14 nSSR (corresponding to 15 diploid genotypes, see above), with the lowest number observed in Banda (N A = 68) and the highest in Bacan (N A = 176). The mean number of alleles per population (N M) ranged from 5.00 to 11.73 across the five populations (Table 1). We found a lower genetic diversity in Ambon and Banda than in Ternate, Tidore and Bacan, as shown by the rarefied allelic richness statistics (AR (k=46), Table 1). The inbreeding coefficient (F IS) values were found to be significantly greater than zero in Ambon, Ternate, and Bacan, indicating a signal of inbreeding.
The global genetic structure among populations as measured by theF ST was 0.069. Meanwhile, the pairwiseF ST between populations ranged from 0.012 (between Ternate and Bacan) to 0.182 (between Ambon and Tidore) (Table 2). The genetic structure within populations (F STamong sub-populations) was globally relatively low (F ST values from 0.008 in Bacan to 0.040 in Tidore; see details in Supplementary Table S2).
Bayesian-clustering analyses suggest that the most likely number of intra-specific genetic clusters within our data set is 2 (Supplementary Figure S2). Individuals from Ambon and Banda are assigned to a first genetic cluster (Figure 2A / 2C), referred as the ‘Southern Moluccas cluster’ hereafter, whereas individuals from Ternate, Tidore and Bacan are generally assigned to a second genetic cluster, that we name the ‘Northern Moluccas cluster’ (F ST = 0.089 between the two clusters). A part of these individuals show variable admixture proportions (probability of assignation to a cluster between 0.2 and 0.9) with the Southern Moluccas cluster (31%, 4%, and 26%, respectively for Ternate, Tidore and Bacan).
Our STRUCTURE results also indicate that the Northern Moluccas cluster is further subdivided into two groups at K = 3 (Figure 2), with the first cluster (2a) including Ternate, Tidore, and part of Bacan individuals (78%), and a second cluster (2b) including 22% of individuals from Bacan island (F ST = 0.055 between cluster 2a and 2b). We further investigated this by running an additional analysis in STRUCTURE with individuals from the Northern Moluccas cluster (N = 160), and also Bacan island (N = 75; Supplementary Table S3). This additional analysis indicated K  = 2 as the most plausible solution (Supplementary Figure S3), supporting the subdivision of the North Moluccas cluster into 2a and 2b as observed in the previous analysis.
Genetic diversity and population structure of M. fragrans